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Save ryanlayer/38b58ef08a5ef7dbe326 to your computer and use it in GitHub Desktop.
| WIN=100 | |
| SAMPLE="NA12878" | |
| SAMPLE_BAM="NA12878_S1.bam" | |
| cnvnator -root $SAMPLE.$WIN.root -genome GRCh37 -tree $SAMPLE_BAM | |
| cnvnator -genome GRCh37 -root $SAMPLE.$WIN.root -his $WIN -d /shared/genomes/b37/full/chroms | |
| cnvnator -root $SAMPLE.$WIN.root -stat $WIN | |
| cnvnator -root $SAMPLE.$WIN.root -partition $WIN | |
| cnvnator -root $SAMPLE.$WIN.root -call $WIN > $SAMPLE.$WIN.cnvcalls.txt | |
| ~/src/lumpy-sv/scripts/cnvanator_to_bedpes.py \ | |
| -c NA12878.$WIN.cnvcalls.txt \ | |
| -b 600 \ | |
| --del_o del.$WIN.bedpe \ | |
| --dup_o dup.$WIN.bedpe | |
| #### DEPENDING ON IF YOU BAMS ARE chr1 or 1 YOU MAY NOT NEED THIS STEP | |
| cat del.$WIN.bedpe | sed -e "s/chr//g" > del.$WIN.nochr.bedpe | |
| cat dup.$WIN.bedpe | sed -e "s/chr//g" > dup.$WIN.nochr.bedpe | |
| ~/src/lumpy-sv/scripts/bedpe_sort.py \ | |
| -b del.$WIN.nochr.bedpe \ | |
| -g ~/scratch/cnvnator/genome.txt\ | |
| > del.$WIN.nochr.posSorted.bedpe | |
| ~/src/lumpy-sv/scripts/bedpe_sort.py \ | |
| -b dup.$WIN.nochr.bedpe \ | |
| -g ~/scratch/cnvnator/genome.txt\ | |
| > dup.$WIN.nochr.posSorted.bedpe | |
| ~/src/lumpy-sv/bin/lumpy \ | |
| -mw 4 \ | |
| -tt 1.0 \ | |
| -pe bam_file:$PEBAM,histo_file:$HISTO,mean:$MEAN,stdev:$STD,read_length:100,min_non_overlap:100,discordant_z:$Z,back_distance:20,weight:1,id:PE,min_mapping_threshold:10 \ | |
| -sr bam_file:$SRBAM,back_distance:20,min_mapping_threshold:10,weight:1,id:SR,min_clip:20 \ | |
| -bedpe bedpe_file:dup.$WIN.posSorted.bedpe,weight:3,id:DUP \ | |
| -bedpe bedpe_file:del.$WIN.posSorted.bedpe,weight:3,id:DEL |
How would one incorporate tumor-normal pairs into this workflow? I've tried the following:
$LUMPY -mw 4
-tt 1.0
-pe id:normal,bam_file:$NORMAL_PEBAM,histo_file:$NORMAL_HISTO,mean:$NORMAL_MEAN,stdev:$NORMAL_STD,read_length:100,min_non_overlap:100,discordant_z:$Z,back_distance:20,weight:1,id:PE,min_mapping_threshold:10
-sr id:normal,bam_file:$NORMAL_SRBAM,back_distance:20,min_mapping_threshold:10,weight:1,id:SR,min_clip:20
-pe id:tumor,bam_file:$TUMOR_PEBAM,histo_file:$TUMOR_HISTO,mean:$TUMOR_MEAN,stdev:$TUMOR_STD,read_length:100,min_non_overlap:100,discordant_z:$Z,back_distance:20,weight:1,id:PE,min_mapping_threshold:10
-sr id:tumor,bam_file:$TUMOR_SRBAM,back_distance:20,min_mapping_threshold:10,weight:1,id:SR,min_clip:20
-bedpe id:tumor_dup,bedpe_file:${setdir}/dup.$WIN.tumor.bedpe,weight:4
-bedpe id:tumor_del,bedpe_file:${setdir}/del.$WIN.tumor.bedpe,weight:4 > tumornormal.vcf
But my vcf header contains fields:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PE SR tumor_dup tumor_del
I expected the tumor, normal samples to have separate fields in the header, as they did when I ran lumpy_express. Does the vcf contain information for both samples?
Thanks for your help.
What format should the genome file be in for the bedpe_sort.py script? I tried using the reference genome in fasta format and it returned a blank file.
./bedpe_sort.py -b del.sample.nochr.bedpe -g reference.fasta > del.sample.nochr.posSorted.bedpe
Thank you for this! Life saver :-)