Created
February 7, 2011 18:20
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RS Exome analysis on the PBS environment
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| export BATCH1="1094PC0005 1094PC0009 1094PC0012 1094PC0013 " | |
| export BATCH2="1094PC0016 1094PC0017 1094PC0018 1094PC0019 \ | |
| 1094PC0020 1094PC0021 1094PC0022 1094PC0023 1094PC0025 " | |
| export BATCH3="1478PC0001B 1478PC0002 1478PC0003 1478PC0004 \ | |
| 1478PC0005 1478PC0006B 1478PC0007B 1478PC0008B \ | |
| 1478PC0009B 1478PC0010 1478PC0011 1478PC0012 \ | |
| 1478PC0013B 1478PC0014B 1478PC0015B 1478PC0016 \ | |
| 1478PC0017B 1478PC0018 1478PC0019 1478PC0020 \ | |
| 1478PC0021 1478PC0022B 1478PC0023B 1478PC0024B" | |
| export BATCH4="1719PC0001 1719PC0002 1719PC0003 1719PC0004 \ | |
| 1719PC0005 1719PC0006 1719PC0007 1719PC0008 \ | |
| 1719PC0009 1719PC0010 1719PC0011 1719PC0012 \ | |
| 1719PC0013 1719PC0014 1719PC0015 1719PC0016 \ | |
| 1719PC0017 1719PC0018 1719PC0019 1719PC0020 \ | |
| 1719PC0021 1719PC0022" | |
| export ALL="1094PC0005 1094PC0009 1094PC0012 1094PC0013 \ | |
| 1094PC0016 1094PC0017 1094PC0018 1094PC0019 \ | |
| 1094PC0020 1094PC0021 1094PC0022 1094PC0023 1094PC0025 \ | |
| 1478PC0001B 1478PC0002 1478PC0003 1478PC0004 \ | |
| 1478PC0005 1478PC0006B 1478PC0007B 1478PC0008B \ | |
| 1478PC0009B 1478PC0010 1478PC0011 1478PC0012 \ | |
| 1478PC0013B 1478PC0014B 1478PC0015B 1478PC0016 \ | |
| 1478PC0017B 1478PC0018 1478PC0019 1478PC0020 \ | |
| 1478PC0021 1478PC0022B 1478PC0023B 1478PC0024B \ | |
| 1478PC0025 \ | |
| 1719PC0001 1719PC0002 1719PC0003 1719PC0004 \ | |
| 1719PC0005 1719PC0006 1719PC0007 1719PC0008 \ | |
| 1719PC0009 1719PC0010 1719PC0011 1719PC0012 \ | |
| 1719PC0013 1719PC0014 1719PC0015 1719PC0016 \ | |
| 1719PC0017 1719PC0018 1719PC0019 1719PC0020 \ | |
| 1719PC0021 1719PC0022" | |
| export LAST="1478PC0025" | |
| ############################################################ | |
| # Convert latest batch. | |
| ############################################################ | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_2_SL16528.fastq C0UPMACXX_s2_1_GSL48index_2_SL16528.fastq > 1719-PC-0001.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_2_SL16528.fastq C0UPMACXX_s2_2_GSL48index_2_SL16528.fastq > 1719-PC-0001.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_3_SL16529.fastq C0UPMACXX_s2_1_GSL48index_3_SL16529.fastq > 1719-PC-0002.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_3_SL16529.fastq C0UPMACXX_s2_2_GSL48index_3_SL16529.fastq > 1719-PC-0002.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_4_SL16530.fastq C0UPMACXX_s2_1_GSL48index_4_SL16530.fastq > 1719-PC-0003.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_4_SL16530.fastq C0UPMACXX_s2_2_GSL48index_4_SL16530.fastq > 1719-PC-0003.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_5_SL16531.fastq C0UPMACXX_s2_1_GSL48index_5_SL16531.fastq > 1719-PC-0004.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_5_SL16531.fastq C0UPMACXX_s2_2_GSL48index_5_SL16531.fastq > 1719-PC-0004.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_6_SL16532.fastq C0UPMACXX_s2_1_GSL48index_6_SL16532.fastq > 1719-PC-0005.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_6_SL16532.fastq C0UPMACXX_s2_2_GSL48index_6_SL16532.fastq > 1719-PC-0005.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_7_SL16533.fastq C0UPMACXX_s2_1_GSL48index_7_SL16533.fastq > 1719-PC-0006.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_7_SL16533.fastq C0UPMACXX_s2_2_GSL48index_7_SL16533.fastq > 1719-PC-0006.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_8_SL16534.fastq C0UPMACXX_s2_1_GSL48index_8_SL16534.fastq > 1719-PC-0007.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_8_SL16534.fastq C0UPMACXX_s2_2_GSL48index_8_SL16534.fastq > 1719-PC-0007.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_1_GSL48index_9_SL16535.fastq C0UPMACXX_s2_1_GSL48index_9_SL16535.fastq > 1719-PC-0008.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s1_2_GSL48index_9_SL16535.fastq C0UPMACXX_s2_2_GSL48index_9_SL16535.fastq > 1719-PC-0008.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_10_SL16536.fastq C0UPMACXX_s4_1_GSL48index_10_SL16536.fastq > 1719-PC-0009.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_10_SL16536.fastq C0UPMACXX_s4_2_GSL48index_10_SL16536.fastq > 1719-PC-0009.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_11_SL16537.fastq C0UPMACXX_s4_1_GSL48index_11_SL16537.fastq > 1719-PC-0010.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_11_SL16537.fastq C0UPMACXX_s4_2_GSL48index_11_SL16537.fastq > 1719-PC-0010.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_12_SL16538.fastq C0UPMACXX_s4_1_GSL48index_12_SL16538.fastq > 1719-PC-0011.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_12_SL16538.fastq C0UPMACXX_s4_2_GSL48index_12_SL16538.fastq > 1719-PC-0011.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_1_SL16539.fastq C0UPMACXX_s4_1_GSL48index_1_SL16539.fastq > 1719-PC-0012.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_1_SL16539.fastq C0UPMACXX_s4_2_GSL48index_1_SL16539.fastq > 1719-PC-0012.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_2_SL16540.fastq C0UPMACXX_s4_1_GSL48index_2_SL16540.fastq > 1719-PC-0013.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_2_SL16540.fastq C0UPMACXX_s4_2_GSL48index_2_SL16540.fastq > 1719-PC-0013.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_3_SL16541.fastq C0UPMACXX_s4_1_GSL48index_3_SL16541.fastq > 1719-PC-0014.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_3_SL16541.fastq C0UPMACXX_s4_2_GSL48index_3_SL16541.fastq > 1719-PC-0014.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_4_SL16542.fastq C0UPMACXX_s4_1_GSL48index_4_SL16542.fastq > 1719-PC-0015.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_4_SL16542.fastq C0UPMACXX_s4_2_GSL48index_4_SL16542.fastq > 1719-PC-0015.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_1_GSL48index_5_SL16543.fastq C0UPMACXX_s4_1_GSL48index_5_SL16543.fastq > 1719-PC-0016.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s3_2_GSL48index_5_SL16543.fastq C0UPMACXX_s4_2_GSL48index_5_SL16543.fastq > 1719-PC-0016.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_1_GSL48index_6_SL16544.fastq C0UPMACXX_s6_1_GSL48index_6_SL16544.fastq > 1719-PC-0017.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_2_GSL48index_6_SL16544.fastq C0UPMACXX_s6_2_GSL48index_6_SL16544.fastq > 1719-PC-0017.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_1_GSL48index_7_SL16545.fastq C0UPMACXX_s6_1_GSL48index_7_SL16545.fastq > 1719-PC-0018.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_2_GSL48index_7_SL16545.fastq C0UPMACXX_s6_2_GSL48index_7_SL16545.fastq > 1719-PC-0018.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_1_GSL48index_8_SL16546.fastq C0UPMACXX_s6_1_GSL48index_8_SL16546.fastq > 1719-PC-0019.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_2_GSL48index_8_SL16546.fastq C0UPMACXX_s6_2_GSL48index_8_SL16546.fastq > 1719-PC-0019.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_1_GSL48index_9_SL16547.fastq C0UPMACXX_s6_1_GSL48index_9_SL16547.fastq > 1719-PC-0020.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_2_GSL48index_9_SL16547.fastq C0UPMACXX_s6_2_GSL48index_9_SL16547.fastq > 1719-PC-0020.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_1_GSL48index_10_SL16548.fastq C0UPMACXX_s6_1_GSL48index_10_SL16548.fastq > 1719-PC-0021.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_2_GSL48index_10_SL16548.fastq C0UPMACXX_s6_2_GSL48index_10_SL16548.fastq > 1719-PC-0021.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_1_GSL48index_11_SL16549.fastq C0UPMACXX_s6_1_GSL48index_11_SL16549.fastq > 1719-PC-0022.1.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/origFromHudsonAlpha/2012-Sept; cat C0UPMACXX_s5_2_GSL48index_11_SL16549.fastq C0UPMACXX_s6_2_GSL48index_11_SL16549.fastq > 1719-PC-0022.2.fq" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=1000m:ncpus=1 | |
| ############################################################ | |
| # Quick hack to ensure no sample mix-ups. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-proper | |
| for sample in `echo $BATCH3` | |
| do | |
| # -m ea sends an email when job (e)nds or (a)borts | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=2 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools view -q 20 -f 2 -u origFromHudsonAlpha/$sample.bam \ | |
| | intersectBed -abam stdin -b bed/sureselect.liftedTohg19.slop500.numchroms.bed \ | |
| > bam/$sample.conc.on.bam" | $QSUB | |
| done | |
| ###################################### | |
| # Sort the original BAM files by name: | |
| ###################################### | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-nmsrt | |
| for sample in `echo $BATCH4` | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=6000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools sort -n -m 2000000000 origFromHudsonAlpha/$sample.bam bam/$sample.namesorted" | $QSUB | |
| done | |
| ############################################################ | |
| # Create new FASTQ files for every sample | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-b2fq | |
| for sample in `echo $BATCH4`; | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx2g -jar /home/arq5x/cphg-home/bin/SamToFastq.jar \ | |
| INPUT=bam/$sample.namesorted.bam \ | |
| VALIDATION_STRINGENCY=LENIENT \ | |
| F=fastq/$sample.1.fq \ | |
| F2=fastq/$sample.2.fq" | $QSUB; | |
| done | |
| ############################################################ | |
| # Gzip the FASTQs | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-fqzip | |
| for sample in `echo $BATCH4`; | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; gzip fastq/$sample.1.fq" | $QSUB; | |
| echo "cd $RSHOME; gzip fastq/$sample.2.fq" | $QSUB; | |
| done | |
| ########################################## | |
| # Delete the name-sorted BAMs | |
| ########################################## | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| for sample in `echo $BATCH4` | |
| do | |
| cd $RSHOME; rm bam/$sample.namesorted.bam | |
| done | |
| ########################################## | |
| # Align the raw FASTQ with BWA | |
| ########################################## | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-bwa-aln | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| for sample in `echo $BATCH4` | |
| do | |
| # -m ea sends an email when job (e)nds or (a)borts | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=8 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; bwa aln -e 1 -t 8 $GENOME fastq/$sample.1.fq > bam/$sample.1.sai" | $QSUB | |
| echo "cd $RSHOME; bwa aln -e 1 -t 8 $GENOME fastq/$sample.2.fq > bam/$sample.2.sai" | $QSUB | |
| done | |
| ############################################################ | |
| # Pair the alignments. | |
| # Keep proper, on-target (i.e. +/- 500 bp of a probe) pairs. | |
| # Require mapping quality >= 20 | |
| # Add the sample ID as a RG | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-bwa-pair | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| for sample in `echo $BATCH4` | |
| do | |
| # -m ea sends an email when job (e)nds or (a)borts | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=3 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; bwa sampe -r '@RG\tID:$sample\tSM:$sample' $GENOME bam/$sample.1.sai bam/$sample.2.sai fastq/$sample.1.fq fastq/$sample.2.fq \ | |
| | samtools view -q 20 -f 2 -Su - \ | |
| | intersectBed -abam stdin -b bed/sureselect.liftedTohg19.slop500.bed \ | |
| > bam/$sample.conc.on.bam" | $QSUB | |
| done | |
| ###################################### | |
| # Data quality assessment - flagstat: | |
| ###################################### | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-flagstat | |
| for sample in `echo $ALL` | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools flagstat origFromHudsonAlpha/$sample.bam > origFromHudsonAlpha/$sample.bam.flagstat" | $QSUB | |
| done | |
| ########################################################## | |
| # Data quality assessment - flagstat for conc, on-target: | |
| ########################################################## | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-conc-fs | |
| for sample in `echo $ALL` | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools flagstat bam/$sample.conc.on.bam > bam/$sample.conc.on.bam.flagstat" | $QSUB | |
| done | |
| ###################################### | |
| # Data quality assessment - coverage: | |
| ###################################### | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-cov | |
| export SAMPLES="1094PC0005 1094PC0009 1094PC0012 1094PC0013 1094PC0016 1094PC0017 1094PC0018 1094PC0019 1094PC0020 1094PC0021 1094PC0022 1094PC0023 1094PC0025" | |
| for sample in `echo $SAMPLES` | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; coverageBed -abam bam/$sample.conc.on.bam -b bed/sureselect.liftedTohg19.slop500.bed > bam/$sample.conc.on.bam.cov" | $QSUB | |
| done | |
| ###################################### | |
| # Data quality assessment - err. rate: | |
| ###################################### | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-err | |
| export SAMPLES="1094PC0005 1094PC0009 1094PC0012 1094PC0013 1094PC0016 1094PC0017 1094PC0018 1094PC0019 1094PC0020 1094PC0021 1094PC0022 1094PC0023 1094PC0025" | |
| for sample in `echo $SAMPLES` | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; bamToBed -i bam/$sample.conc.on.bam -tag NM | head -1000000 | cut -f 5 | stats > bam/$sample.conc.on.bam.err" | $QSUB | |
| done | |
| ############################################################ | |
| # Sort the on-target concordants by genome position. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-possrt | |
| for sample in `echo $BATCH4` | |
| do | |
| # -m ea sends an email when job (e)nds or (a)borts | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=12000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools sort -m 4000000000 bam/$sample.conc.on.bam bam/$sample.conc.on.pos" | $QSUB | |
| done | |
| ############################################################ | |
| # Index the position-sorted BAM files. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-index | |
| for sample in `echo $BATCH4` | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools index bam/$sample.conc.on.pos.bam" | $QSUB | |
| done | |
| ############################################################ | |
| # Use mpileup to get a snese of any sample mix-ups | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-mpile | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export SAMPLES="bam/1094PC0005.conc.on.pos.bam \ | |
| bam/1094PC0009.conc.on.pos.bam \ | |
| bam/1094PC0012.conc.on.pos.bam \ | |
| bam/1094PC0013.conc.on.pos.bam \ | |
| bam/1094PC0016.conc.on.pos.bam \ | |
| bam/1094PC0017.conc.on.pos.bam \ | |
| bam/1094PC0018.conc.on.pos.bam \ | |
| bam/1094PC0019.conc.on.pos.bam \ | |
| bam/1094PC0020.conc.on.pos.bam \ | |
| bam/1094PC0021.conc.on.pos.bam \ | |
| bam/1094PC0022.conc.on.pos.bam \ | |
| bam/1094PC0023.conc.on.pos.bam \ | |
| bam/1094PC0025.conc.on.pos.bam \ | |
| bam/1478PC0017B.conc.on.bam \ | |
| bam/1478PC0012.conc.on.bam \ | |
| bam/1478PC0024B.conc.on.bam \ | |
| bam/1478PC0004.conc.on.bam \ | |
| bam/1478PC0003.conc.on.bam \ | |
| bam/1478PC0018.conc.on.bam \ | |
| bam/1478PC0009B.conc.on.bam \ | |
| bam/1478PC0010.conc.on.bam \ | |
| bam/1478PC0013B.conc.on.bam \ | |
| bam/1478PC0011.conc.on.bam \ | |
| bam/1478PC0019.conc.on.bam \ | |
| bam/1478PC0007B.conc.on.bam \ | |
| bam/1478PC0022B.conc.on.bam \ | |
| bam/1478PC0015B.conc.on.bam \ | |
| bam/1478PC0021.conc.on.bam \ | |
| bam/1478PC0014B.conc.on.bam \ | |
| bam/1478PC0005.conc.on.bam \ | |
| bam/1478PC0001B.conc.on.bam \ | |
| bam/1478PC0006B.conc.on.bam \ | |
| bam/1478PC0008B.conc.on.bam \ | |
| bam/1478PC0016.conc.on.bam \ | |
| bam/1478PC0002.conc.on.bam \ | |
| bam/1478PC0023B.conc.on.bam \ | |
| bam/1478PC0020.conc.on.bam" | |
| # -m ea sends an email when job (e)nds or (a)borts | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools mpileup -uf $GENOME $SAMPLES | bcftools view -bvcg - > varCalling/2012-Jan/kinship-quick/var.mpileup.raw.bcf" | $QSUB | |
| ############################################################ | |
| # Mark duplicates | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-dupe | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export BIN=/home/arq5x/cphg-home/shared/bin/picard-tools-1.60 | |
| for sample in `echo $BATCH4`; | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=2 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx2g -jar $BIN/MarkDuplicates.jar \ | |
| INPUT=bam/$sample.conc.on.pos.bam \ | |
| OUTPUT=bam/$sample.conc.on.pos.dedup.bam \ | |
| TMP_DIR=$RSHOME/bam \ | |
| VALIDATION_STRINGENCY=LENIENT \ | |
| ASSUME_SORTED=true \ | |
| METRICS_FILE=bam/$sample.markdup_metrics" | $QSUB; | |
| done | |
| ############################################################ | |
| # Index the position-sorted, deduped BAM files. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-index | |
| for sample in `echo $BATCH4` | |
| do | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=2000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools index bam/$sample.conc.on.pos.dedup.bam" | $QSUB | |
| done | |
| ############################################################ | |
| # Merge BAM files | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rs-ex-merge | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export BIN=/home/arq5x/cphg-home/shared/bin/picard-tools-1.60 | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=4 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx2g -jar $BIN/MergeSamFiles.jar \ | |
| O=bam/all.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0005.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0009.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0012.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0013.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0016.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0017.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0018.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0019.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0020.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0021.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0022.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0023.conc.on.pos.dedup.bam \ | |
| I=bam/1094PC0025.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0001B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0002.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0003.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0004.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0005.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0006B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0007B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0008B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0009B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0010.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0011.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0012.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0013B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0014B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0015B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0016.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0017B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0018.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0019.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0020.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0021.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0022B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0023B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0024B.conc.on.pos.dedup.bam \ | |
| I=bam/1478PC0025.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0001.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0002.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0003.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0004.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0005.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0006.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0007.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0008.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0009.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0010.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0011.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0012.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0013.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0014.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0015.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0016.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0017.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0018.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0019.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0020.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0021.conc.on.pos.dedup.bam \ | |
| I=bam/1719PC0022.conc.on.pos.dedup.bam \ | |
| TMP_DIR=$RSHOME/bam \ | |
| USE_THREADING=true" | $QSUB; | |
| ############################################################ | |
| # Identify realignment targets. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-realtgts | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export BIN=/home/arq5x/cphg-home/shared/bin/GenomeAnalysisTK-1.4-9-g1f1233b | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=3 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx2g -jar $BIN/GenomeAnalysisTK.jar \ | |
| -T RealignerTargetCreator \ | |
| -R $GENOME \ | |
| -I bam/all.conc.on.pos.dedup.bam \ | |
| -o bam/all.conc.on.pos.dedup.bam.intervals" | $QSUB; | |
| ############################################################ | |
| # Use GATK to realign the BAMs at the suspicious targets. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-realtgts | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export BIN=/home/arq5x/cphg-home/shared/bin/GenomeAnalysisTK-1.4-9-g1f1233b | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=4 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx2g -Djava.io.tmpdir=$RSHOME/bam -jar $BIN/GenomeAnalysisTK.jar \ | |
| -T IndelRealigner \ | |
| --num_threads 1 \ | |
| -R $GENOME \ | |
| -targetIntervals bam/all.conc.on.pos.dedup.bam.intervals \ | |
| -I bam/all.conc.on.pos.dedup.bam \ | |
| -o bam/all.conc.on.pos.dedup.realigned.bam" | $QSUB; | |
| ############################################################ | |
| # Index the merged, deduped BAM file as well as the | |
| # merged, deduped, realigned file. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-index | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=4000m:ncpus=4 -N $STEPNAME -m bea -M [email protected]" | |
| echo "cd $RSHOME; samtools index bam/all.conc.on.pos.dedup.bam" | $QSUB | |
| echo "cd $RSHOME; samtools index bam/all.conc.on.pos.dedup.realigned.bam" | $QSUB | |
| ############################################################ | |
| # Call SNPs and INDELs with GATK using BAQ. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-varbaq | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export BIN=/home/arq5x/cphg-home/shared/bin/GenomeAnalysisTK-1.4-9-g1f1233b | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=12 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx2g -jar $BIN/GenomeAnalysisTK.jar \ | |
| -T UnifiedGenotyper \ | |
| -glm BOTH \ | |
| --num_threads 10 \ | |
| -baq CALCULATE_AS_NECESSARY \ | |
| -R $GENOME \ | |
| -I bam/all.conc.on.pos.dedup.realigned.bam \ | |
| -o varCalling/2012-Nov-09/all.raw.baq.vcf" | $QSUB; | |
| ############################################################ | |
| # Call SNPs and INDELs with GATK W/O using BAQ. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-varbaq | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export BIN=/home/arq5x/cphg-home/shared/bin/GenomeAnalysisTK-1.4-9-g1f1233b | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=12 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx2g -jar $BIN/GenomeAnalysisTK.jar \ | |
| -T UnifiedGenotyper \ | |
| -glm BOTH \ | |
| --num_threads 10 \ | |
| -baq OFF \ | |
| -R $GENOME \ | |
| -I bam/all.conc.on.pos.dedup.realigned.bam \ | |
| -o varCalling/2012-Nov-09/all.raw.nobaq.vcf" | $QSUB; | |
| ############################################################ | |
| # Call INDELs with GATK. | |
| ############################################################ | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-callsnps | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export SAMPLES="1094PC0005 1094PC0009 1094PC0012 1094PC0013 1094PC0016 1094PC0017 1094PC0018 1094PC0019 1094PC0020 1094PC0021 1094PC0022 1094PC0023 1094PC0025" | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=8000m:ncpus=4 -N $STEPNAME -m bea -M [email protected]"; | |
| for sample in `echo $SAMPLES`; | |
| do | |
| echo "cd $RSHOME; java -Xmx4g -jar /home/arq5x/cphg-home/bin/GenomeAnalysisTK.jar \ | |
| -T IndelGenotyperV2 \ | |
| -l INFO \ | |
| -R $GENOME \ | |
| -I bam/$sample.conc.on.pos.realigned.dedup.baq.bam \ | |
| -o varCalling/$sample.indel.vcf" | $QSUB; | |
| done | |
| ######################################################################## | |
| # Combine the INDEL call from each sample into a single file with GATK. | |
| ######################################################################## | |
| export RSHOME=/home/arq5x/cphg-home/projects/rs-exome | |
| export STEPNAME=rsex-callsnps | |
| export GENOME=/home/arq5x/cphg-home/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa | |
| export QSUB="qsub -q cphg -W group_list=CPHG -V -l select=1:mem=16000m:ncpus=2 -N $STEPNAME -m bea -M [email protected]"; | |
| echo "cd $RSHOME; java -Xmx10g -jar /home/arq5x/cphg-home/bin/GenomeAnalysisTK.jar \ | |
| -T CombineVariants \ | |
| -R $GENOME \ | |
| -o varCalling/indels.raw.vcf \ | |
| -variantMergeOptions UNION \ | |
| -genotypeMergeOptions UNIQUIFY \ | |
| -B:1094PC0005,VCF varCalling/1094PC0005.indel.vcf \ | |
| -B:1094PC0009,VCF varCalling/1094PC0009.indel.vcf \ | |
| -B:1094PC0012,VCF varCalling/1094PC0012.indel.vcf \ | |
| -B:1094PC0013,VCF varCalling/1094PC0013.indel.vcf \ | |
| -B:1094PC0016,VCF varCalling/1094PC0016.indel.vcf \ | |
| -B:1094PC0017,VCF varCalling/1094PC0017.indel.vcf \ | |
| -B:1094PC0018,VCF varCalling/1094PC0018.indel.vcf \ | |
| -B:1094PC0019,VCF varCalling/1094PC0019.indel.vcf \ | |
| -B:1094PC0020,VCF varCalling/1094PC0020.indel.vcf \ | |
| -B:1094PC0021,VCF varCalling/1094PC0021.indel.vcf \ | |
| -B:1094PC0022,VCF varCalling/1094PC0022.indel.vcf \ | |
| -B:1094PC0023,VCF varCalling/1094PC0023.indel.vcf \ | |
| -B:1094PC0025,VCF varCalling/1094PC0025.indel.vcf " | $QSUB; | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/varCalling/; annotateVcf.py -i snps.raw.vcf -p /home/arq5x/cphg-home/bin/annovar/ -s /home/arq5x/cphg-home/shared/annotations/hg19/dbSNP/dbsnp.131.hg19.bed -a /home/arq5x/cphg-home/shared/data/exomes/1000G-210Exomes-20110214/ALL.broad_exome.20110124.both.sites.vcf -o /home/arq5x/cphg-home/projects/rs-exome/varCalling/" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=12000m:ncpus=1 -N snp -m bea -M [email protected] | |
| echo "cd /home/arq5x/cphg-home/projects/rs-exome/varCalling/; annotateVcf.py -i indels.raw.vcf -p /home/arq5x/cphg-home/bin/annovar/ -s /home/arq5x/cphg-home/shared/annotations/hg19/dbSNP/dbsnp.131.hg19.bed -a /home/arq5x/cphg-home/shared/data/exomes/1000G-210Exomes-20110214/ALL.broad_exome.20110124.both.sites.vcf -o /home/arq5x/cphg-home/projects/rs-exome/varCalling/" | qsub -q cphg -W group_list=CPHG -V -l select=1:mem=12000m:ncpus=1 -N indel -m bea -M [email protected] | |
| # combine the output of snps and indel annotations into a single file | |
| cat snps.raw.vcf.1.annovar_anno.2.dbsnp_anno.3.vcf_anno indels.raw.vcf.1.annovar_anno.2.dbsnp_anno.3.vcf_anno > all.vcf.anno | |
| # move the file to my laptop | |
| scp elder.itc.virginia.edu:~/cphg-home/projects/rs-exome/varCalling/all.vcf.anno all.vcf.anno.txt | |
| # extract some add'l information from the VCF INFO field | |
| perl -lane 'if (/DP=(\d+)/) {print $1} else {print "-1"}' all.vcf.anno.txt > depths.txt | |
| perl -lane 'if (/HRun=(\d+)/) {print $1} else {print "-1"}' all.vcf.anno.txt > hruns.txt | |
| perl -lane 'if (/AF=(\d.\d+)/) {print $1} else {print "-1"}' all.vcf.anno.txt > dafs.txt | |
| perl -lane 'if (/MQ=(\d+.\d+)/) {print $1} else {print "-1"}' all.vcf.anno.txt > mapqs.txt | |
| # add the extra fields. | |
| paste depths.txt mapqs.txt dafs.txt hruns.txt all.vcf.anno.txt > all.vcf.anno.info.txt | |
| # require: at least 100 reads | |
| # mapq>=30 | |
| # no intronic, intergenic, upstream, downstream or synonymous | |
| awk '$1>=100 && $2 >30' all.vcf.anno.info.txt | \ | |
| grep -v intronic | \ | |
| grep -v intergenic | \ | |
| grep -v upstream | \ | |
| grep -v downstream > \ | |
| all.vcf.anno.info.final.txt |
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