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Splitting .vcf file
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12 months ago
F ♦ 3.4k
Iran

Sorry I got confused again

By strelka I have called SNV on my samples

`./configureStrelkaSomaticWorkflow.py --normalBam /1.bam --tumorBam /2.bam --referenceFasta /hs37d5.fa --runDir demo`

Now I have a .vcf file in results

I tried


    [fi1d18@cyan02 fi1d18]$ bcftools query -l /somatic.snvs.vcf
    NORMAL
    TUMOR

I want two .vcf files for my samples because I need to check the consistency of mutations in two paired samples

I tried

I thought about splitting the resulted .vcf ``

[fi1d18@cyan02 fi1d18]$ vcf-subset -c NORMAL /somatic.snvs.vcf > NORMAL.vcf`

``` But nothing happens, am I doing wrong that I think for checking the consistency of mutations in two paired samples I should split my resulted .vcf file? How I could split this .vcf to samples please?

Then I used vcfkeepsamples/vcfremovesamples utilities from VCFlib toolkit to select my samples one by one although I am not sure at all if I am correct

WGS vcftools • 275 views
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try: bcftools view -Ou -s NORMAL somatic.snvs.vcf F

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[fi1d18@cyan01 fi1d18]$ bcftools view -Ou -s NORMAL /home/fi1d18/demo_somatic_fereshteh1/results/variants/somatic.snvs.vcf
BCF▒%##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed",IDX=0>
##fileDate=20190308
##source=strelka
##source_version=2.9.2
##startTime=Fri Mar  8 17:40:39 2019
##cmdline=/temp/hgig/fi1d18/strelka-2.9.2.centos6_x86_64/bin/configureStrelkaSomaticWorkflow.py --normalBam /temp/hgig/fi1d18/1672_WTSI-OESO_005_w3/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_005_w3.dupmarked.bam --tumorBam /temp/hgig/fi1d18/1672_WTSI-OESO_005_a_RNA/mapped_sample/HUMAN_1000Genomes_hs37d5_RNA_seq_WTSI-OESO_005_a_RNA.dupmarked.bam --referenceFasta /temp/hgig/fi1d18/hs37d5.fa --runDir demo_somatic_fereshteh1
##reference=file:///temp/hgig/fi1d18/hs37d5.fa
##contig=<ID=1,length=249250621,IDX=0>
##contig=<ID=2,length=243199373,IDX=1>
##contig=<ID=3,length=198022430,IDX=2>

And continuing to printing weird lines yet

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@ F Send the output to a file.

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