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arq5x/cell-line-workflow.sh

Last active December 31, 2015 21:39
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Ovarian cancer chemoresistance.
Raw
cell-line-workflow.sh
export SAMPLES="2484-AJ-0001 2484-AJ-0002 2484-AJ-0003"
######################################
# Make FASTQ
######################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
export STEPNAME=ovc-fastq
for sample in `echo $SAMPLES`
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; ~/shared/bin/bamUtil_1.0.9/bamUtil/bin/bam bam2FastQ --in bam/$sample.bam \
--outBase fastq/$sample" | $QSUB;
done
######################################
# GZIP FASTQ
######################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
export STEPNAME=ovc-fastq
for sample in `echo $SAMPLES`
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=1000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; gzip fastq/${sample}_1.fastq" | $QSUB;
echo "cd $OVHOME; gzip fastq/${sample}_2.fastq" | $QSUB;
done
############################################################
# BWA MEM
############################################################
export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes/fasta/human_g1k_v37.fasta
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
export STEPNAME=ovc-bwamem
for sample in `echo $SAMPLES`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=8 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; bwa mem $GENOME fastq/${sample}_1.fastq.gz fastq/${sample}_2.fastq.gz -t 7 -M -R $'@RG\tID:$sample\tSM:$sample' | samtools view -Sb - > bam/$sample.bwamem.bam" | $QSUB
done
############################################################
# SORT
############################################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
export STEPNAME=ov-sort
for sample in `echo $SAMPLES`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=24000m:ncpus=8 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; samtools sort -@ 4 -m 2G bam/$sample.bwamem.bam bam/$sample.bwamem.sort" | $QSUB
done
############################################################
# MARK DUPLICATES
############################################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
export STEPNAME=ov-dedup
export BIN=/home/arq5x/cphg-home/shared/bin/picard-tools-1.72/
for sample in `echo $SAMPLES`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=6 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; java -Xmx2g -jar $BIN/MarkDuplicates.jar \
INPUT=bam/$sample.bwamem.sort.bam \
OUTPUT=bam/$sample.bwamem.sort.dedup.bam \
TMP_DIR=$OVHOME/bam \
VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true \
METRICS_FILE=bam/$sample.markdup_metrics" | $QSUB;
done
############################################################
# FREEBAYES
############################################################
export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes/fasta/human_g1k_v37.fasta
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-cell-lines
export STEPNAME=ov-freeb
for chrom in {1..22} X Y
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=24000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; freebayes-9.9.2 -f $GENOME \
--region $chrom \
--pooled-discrete \
--pooled-continuous \
--min-alternate-fraction 0.05 \
--genotype-qualities \
--report-genotype-likelihood-max \
bam/2484-AJ-0001.bwamem.sort.dedup.bam \
bam/2484-AJ-0002.bwamem.sort.dedup.bam \
bam/2484-AJ-0003.bwamem.sort.dedup.bam \
> varcalling/freebayes.$chrom.minaaf.5pct.vcf" | $QSUB
done
############################################################
# Combine files and remove poor quality variants.
############################################################
(cat freebayes.1.minaaf.5pct.vcf; cat freebayes*.minaaf.5pct.vcf | grep -v ^# | awk '$1 != "1"') \
| vcffilter -f 'QUAL > 1' -f 'DP > 20' -f 'AO > 2' > freebayes.all.minaaf.5pct.filtered.vcf
Raw
copy-number-seg.sh
############################################################
# counts in windows
############################################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-idx
cd $OVHOME;
for sample in `ls bam/*.bwamem.sort.dedup.bam`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=4000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; bedtools intersect -c -sorted -a doc/hg19.500K.windows.gatk.bed -b $sample -g doc/hg19.chrom.order > $sample.500k.bedg" | $QSUB
done
Raw
plot-somatic-allele-freqs.R
setwd("/Users/arq5x/Documents/Projects/QuinlanLab/Collaboration/Jazaeri-OV-Exome/OV-Exome/clonal-evolution")
som <- read.table('somatics.depth.20.nonormals.txt')
# compute the tumor and resistant allele freqs
som$tum_freq <- som[,17] / (som[,17] + som[,14])
som$res_freq <- som[,18] / (som[,18] + som[,15])
# 4x4 plotting grid
par(mfrow=c(4,4))
# plot each sample on the grid
for (sample in unique(sort(som[,1]))) { # extract the unique sample ids in sorted order
sample_rows <- som[,1]==sample
subset <- som[sample_rows,]
plot(subset$tum_freq, subset$res_freq,
main=sample, xlim=c(0,1.0), ylim=c(0,1.0),
xlab="Tumor Freq.", ylab="Resistant Freq.")
}
Raw
prepare-normal-fastq.sh
zcat normals/H7G5DADXX_s1_1_GSLv2-7_74_SL58275.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_74_SL58275.fastq.gz | gzip > s02-N-2379-AJ-0030_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_74_SL58275.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_74_SL58275.fastq.gz | gzip > s02-N-2379-AJ-0030_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_75_SL58276.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_75_SL58276.fastq.gz | gzip > s03-N-2379-AJ-0031_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_75_SL58276.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_75_SL58276.fastq.gz | gzip > s03-N-2379-AJ-0031_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_76_SL58277.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_76_SL58277.fastq.gz | gzip > s04-N-2379-AJ-0032_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_76_SL58277.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_76_SL58277.fastq.gz | gzip > s04-N-2379-AJ-0032_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_77_SL58278.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_77_SL58278.fastq.gz | gzip > s09-N-2379-AJ-0033_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_77_SL58278.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_77_SL58278.fastq.gz | gzip > s09-N-2379-AJ-0033_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_78_SL58279.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_78_SL58279.fastq.gz | gzip > s10-N-2379-AJ-0034_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_78_SL58279.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_78_SL58279.fastq.gz | gzip > s10-N-2379-AJ-0034_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_79_SL58280.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_79_SL58280.fastq.gz | gzip > s11-N-2379-AJ-0035_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_79_SL58280.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_79_SL58280.fastq.gz | gzip > s11-N-2379-AJ-0035_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_80_SL58281.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_80_SL58281.fastq.gz | gzip > s12-N-2379-AJ-0036_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_80_SL58281.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_80_SL58281.fastq.gz | gzip > s12-N-2379-AJ-0036_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_81_SL58282.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_81_SL58282.fastq.gz | gzip > s15-N-2379-AJ-0037_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_81_SL58282.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_81_SL58282.fastq.gz | gzip > s15-N-2379-AJ-0037_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_82_SL58283.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_82_SL58283.fastq.gz | gzip > s17-N-2379-AJ-0038_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_82_SL58283.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_82_SL58283.fastq.gz | gzip > s17-N-2379-AJ-0038_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_83_SL58284.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_83_SL58284.fastq.gz | gzip > s18-N-2379-AJ-0039_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_83_SL58284.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_83_SL58284.fastq.gz | gzip > s18-N-2379-AJ-0039_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_84_SL58285.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_84_SL58285.fastq.gz | gzip > s19-N-2379-AJ-0040_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_84_SL58285.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_84_SL58285.fastq.gz | gzip > s19-N-2379-AJ-0040_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_95_SL58286.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_95_SL58286.fastq.gz | gzip > s20-N-2379-AJ-0041_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_95_SL58286.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_95_SL58286.fastq.gz | gzip > s20-N-2379-AJ-0041_2.fastq.gz &
zcat normals/H7G5DADXX_s1_1_GSLv2-7_96_SL58287.fastq.gz normals/H7G5DADXX_s2_1_GSLv2-7_96_SL58287.fastq.gz | gzip > s21-N-2379-AJ-0042_1.fastq.gz &
zcat normals/H7G5DADXX_s1_2_GSLv2-7_96_SL58287.fastq.gz normals/H7G5DADXX_s2_2_GSLv2-7_96_SL58287.fastq.gz | gzip > s21-N-2379-AJ-0042_2.fastq.gz &
Raw
probe-coverage.sh
############################################################
# counts in windows
############################################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-probecov
cd $OVHOME;
for sample in `ls bam/*.bwamem.sort.dedup.bam`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; bedtools coverage -hist -abam $sample -b bed/SeqCap_EZ_Exome_v3_primary.numeric.bed3 | grep ^all > $sample.probe.cov.hist" | $QSUB
done
Raw
workflow.sh
export ALLSAMPLES="s02-R-2379-AJ-0002 \
s02-T-2379-AJ-0001 \
s03-R-2379-AJ-0004 \
s03-T-2379-AJ-0003 \
s04-R-2379-AJ-0006 \
s04-T-2379-AJ-0005 \
s05-N-2379-AJ-0007 \
s05-R-2379-AJ-0009 \
s05-T-2379-AJ-0008 \
s09-R-2379-AJ-0011 \
s09-T-2379-AJ-0010 \
s10-R-2379-AJ-0013 \
s10-T-2379-AJ-0012 \
s11-R-2379-AJ-0015 \
s11-T-2379-AJ-0014 \
s12-R-2379-AJ-0017 \
s12-T-2379-AJ-0016 \
s15-R-2379-AJ-0019 \
s15-T-2379-AJ-0018 \
s17-R-2379-AJ-0021 \
s17-T-2379-AJ-0020 \
s18-R-2379-AJ-0023 \
s18-T-2379-AJ-0022 \
s19-R-2379-AJ-0025 \
s19-T-2379-AJ-0024 \
s20-R-2379-AJ-0027 \
s20-T-2379-AJ-0026 \
s21-R-2379-AJ-0029 \
s21-T-2379-AJ-0028"
export SAMPLESOLD="s02-R-2379-AJ-0002 \
s02-T-2379-AJ-0001 \
s03-T-2379-AJ-0003 \
s04-R-2379-AJ-0006 \
s04-T-2379-AJ-0005 \
s05-N-2379-AJ-0007 \
s05-R-2379-AJ-0009 \
s05-T-2379-AJ-0008 \
s09-R-2379-AJ-0011 \
s10-R-2379-AJ-0013 \
s10-T-2379-AJ-0012 \
s11-R-2379-AJ-0015 \
s11-T-2379-AJ-0014 \
s12-R-2379-AJ-0017 \
s12-T-2379-AJ-0016 \
s15-R-2379-AJ-0019 \
s15-T-2379-AJ-0018 \
s17-R-2379-AJ-0021 \
s17-T-2379-AJ-0020 \
s18-R-2379-AJ-0023 \
s18-T-2379-AJ-0022 \
s19-R-2379-AJ-0025 \
s19-T-2379-AJ-0024 \
s20-R-2379-AJ-0027 \
s20-T-2379-AJ-0026 \
s21-R-2379-AJ-0029 \
s21-T-2379-AJ-0028"
#export SAMPLES="s03-R-2379-AJ-0004 s09-T-2379-AJ-0010"
export SAMPLES="s02-N-2379-AJ-0030 \
s03-N-2379-AJ-0031 \
s04-N-2379-AJ-0032 \
s09-N-2379-AJ-0033 \
s10-N-2379-AJ-0034 \
s11-N-2379-AJ-0035 \
s12-N-2379-AJ-0036 \
s15-N-2379-AJ-0037 \
s17-N-2379-AJ-0038 \
s18-N-2379-AJ-0039 \
s19-N-2379-AJ-0040 \
s20-N-2379-AJ-0041 \
s21-N-2379-AJ-0042"
######################################
# Sort the original BAM files by name:
######################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-nmsrt
for sample in `echo $SAMPLES`
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=16000m:ncpus=8 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; samtools sort -n -@ 8 -m 1000000000 bam/$sample.bam bam/$sample.namesorted" | $QSUB
done
######################################
# Make FASTQ
######################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-fastq
for sample in `echo $SAMPLES`
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; ~/shared/bin/bamUtil_1.0.9/bamUtil/bin/bam bam2FastQ --in bam/$sample.bam \
--outBase fastq/$sample" | $QSUB;
done
######################################
# GZIP FASTQ
######################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-fastq
for sample in `echo $SAMPLES`
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=1000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; gzip fastq/${sample}_1.fastq" | $QSUB;
echo "cd $OVHOME; gzip fastq/${sample}_2.fastq" | $QSUB;
done
############################################################
# BWA MEM
############################################################
export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes/fasta/human_g1k_v37.fasta
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-bwamem
for sample in `echo $SAMPLES`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=8 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; bwa mem $GENOME fastq/${sample}_1.fastq.gz fastq/${sample}_2.fastq.gz -t 7 -M -R $'@RG\tID:$sample\tSM:$sample' | samtools view -Sb - > bam/$sample.bwamem.bam" | $QSUB
done
############################################################
# SORT
############################################################
export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes/fasta/human_g1k_v37.fasta
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-sort
for sample in `echo $SAMPLES`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=24000m:ncpus=8 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; samtools sort -@ 4 -m 2G bam/$sample.bwamem.bam bam/$sample.bwamem.sort" | $QSUB
done
############################################################
# MARK DUPLICATES
############################################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-dedup
export BIN=/home/arq5x/cphg-home/shared/bin/picard-tools-1.72/
for sample in `echo $SAMPLES`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=8000m:ncpus=6 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; java -Xmx2g -jar $BIN/MarkDuplicates.jar \
INPUT=bam/$sample.bwamem.sort.bam \
OUTPUT=bam/$sample.bwamem.sort.dedup.bam \
TMP_DIR=$OVHOME/bam \
VALIDATION_STRINGENCY=LENIENT \
ASSUME_SORTED=true \
METRICS_FILE=bam/$sample.markdup_metrics" | $QSUB;
done
############################################################
# INDEX
############################################################
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-idx
for sample in `echo $SAMPLES`;
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=1000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; samtools index bam/$sample.bwamem.sort.dedup.bam" | $QSUB
done
############################################################
# FREEBAYES
############################################################
export GENOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes/fasta/human_g1k_v37.fasta
export OVHOME=/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes
export STEPNAME=ov-freeb
for chrom in {1..22} X Y
do
export QSUB="qsub -W group_list=cphg_arq5x -q arq5xlab -V -l select=1:mem=24000m:ncpus=1 -N $STEPNAME -m bea -M [email protected]";
echo "cd $OVHOME; freebayes-9.9.2 -f $GENOME \
--region $chrom \
--pooled-discrete \
--pooled-continuous \
--min-alternate-fraction 0.05 \
--genotype-qualities \
--report-genotype-likelihood-max \
bam/s02-N-2379-AJ-0030.bwamem.sort.dedup.bam \
bam/s02-T-2379-AJ-0001.bwamem.sort.dedup.bam \
bam/s02-R-2379-AJ-0002.bwamem.sort.dedup.bam \
bam/s03-N-2379-AJ-0031.bwamem.sort.dedup.bam \
bam/s03-T-2379-AJ-0003.bwamem.sort.dedup.bam \
bam/s03-R-2379-AJ-0004.bwamem.sort.dedup.bam \
bam/s04-N-2379-AJ-0032.bwamem.sort.dedup.bam \
bam/s04-T-2379-AJ-0005.bwamem.sort.dedup.bam \
bam/s04-R-2379-AJ-0006.bwamem.sort.dedup.bam \
bam/s05-N-2379-AJ-0007.bwamem.sort.dedup.bam \
bam/s05-T-2379-AJ-0008.bwamem.sort.dedup.bam \
bam/s05-R-2379-AJ-0009.bwamem.sort.dedup.bam \
bam/s09-N-2379-AJ-0033.bwamem.sort.dedup.bam \
bam/s09-T-2379-AJ-0010.bwamem.sort.dedup.bam \
bam/s09-R-2379-AJ-0011.bwamem.sort.dedup.bam \
bam/s10-N-2379-AJ-0034.bwamem.sort.dedup.bam \
bam/s10-T-2379-AJ-0012.bwamem.sort.dedup.bam \
bam/s10-R-2379-AJ-0013.bwamem.sort.dedup.bam \
bam/s11-N-2379-AJ-0035.bwamem.sort.dedup.bam \
bam/s11-T-2379-AJ-0014.bwamem.sort.dedup.bam \
bam/s11-R-2379-AJ-0015.bwamem.sort.dedup.bam \
bam/s12-N-2379-AJ-0036.bwamem.sort.dedup.bam \
bam/s12-T-2379-AJ-0016.bwamem.sort.dedup.bam \
bam/s12-R-2379-AJ-0017.bwamem.sort.dedup.bam \
bam/s15-N-2379-AJ-0037.bwamem.sort.dedup.bam \
bam/s15-T-2379-AJ-0018.bwamem.sort.dedup.bam \
bam/s15-R-2379-AJ-0019.bwamem.sort.dedup.bam \
bam/s17-N-2379-AJ-0038.bwamem.sort.dedup.bam \
bam/s17-T-2379-AJ-0020.bwamem.sort.dedup.bam \
bam/s17-R-2379-AJ-0021.bwamem.sort.dedup.bam \
bam/s18-N-2379-AJ-0039.bwamem.sort.dedup.bam \
bam/s18-T-2379-AJ-0022.bwamem.sort.dedup.bam \
bam/s18-R-2379-AJ-0023.bwamem.sort.dedup.bam \
bam/s19-N-2379-AJ-0040.bwamem.sort.dedup.bam \
bam/s19-T-2379-AJ-0024.bwamem.sort.dedup.bam \
bam/s19-R-2379-AJ-0025.bwamem.sort.dedup.bam \
bam/s20-N-2379-AJ-0041.bwamem.sort.dedup.bam \
bam/s20-T-2379-AJ-0026.bwamem.sort.dedup.bam \
bam/s20-R-2379-AJ-0027.bwamem.sort.dedup.bam \
bam/s21-N-2379-AJ-0042.bwamem.sort.dedup.bam \
bam/s21-T-2379-AJ-0028.bwamem.sort.dedup.bam \
bam/s21-R-2379-AJ-0029.bwamem.sort.dedup.bam \
> varcalling/freebayes.$chrom.minaaf.5pct.vcf" | $QSUB
done
############################################################
# Combine files and remove poor quality variants.
############################################################
(cat freebayes.1.minaaf.5pct.vcf; cat freebayes*.minaaf.5pct.vcf | grep -v ^# | awk '$1 != "1"') \
| vcffilter -f 'QUAL > 1' -f 'DP > 200' -f 'AO > 2' > freebayes.all.minaaf.5pct.filtered.vcf
java -Xmx4g -jar snpEff.jar eff -v GRCh37.69 /home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes/varcalling/freebayes.all.minaaf.10pct.vcf >/home/arq5x/cphg-home/cphg-quinlan/projects/ov-chemoresistant-exomes/varcalling/freebayes.all.minaaf.10pct.snpEff.vcf
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