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
try:
bcftools view -Ou -s NORMAL somatic.snvs.vcf
FAnd continuing to printing weird lines yet
@ F Send the output to a file.