Calling CNV using bcftools

Question

[Raheleh]

Hi, I used VarScan2 to call variants from whole exome sequencing data. The vcf file output looks like this:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NORMAL  TUMOR
chr1    972251  .   A   AC  .   PASS    DP=173;SOMATIC;SS=2;SSC=75;GPV=1;SPV=2.5611e-08 GT:GQ:DP:RD:AD:FREQ:DP4 0/0:.:65:63:0:0%:36,27,0,0  0/1:.:108:74:33:30.84%:46,28,18,15

I ran this command of bcftools:

bcftools cnv -c NORMAL -s TUMOR -o outdir/ -p 0 samples_concated.vcf

to get copy number variations, but it returned empty files. Can anyone help me to fix it? Is there any wrong with my vcf file or with my command? Than you!

Answer 1

[Pierre Lindenbaum]

$ bcftools cnv

About: Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R

Ratio intensity (LRR). The HMM considers the following copy number states: CN 2

both annotations are missing in your VCF.

[Raheleh]

@Pierre Lindenbaum Dear Pierre many thanks for your reply. How can I get these two annotations for my data. Should I use another variant caller instead of VarScan2? If so, what do you recommend?

[Waly]

I recommend this training to understand more: https://support.illumina.com/array/array_software/genomestudio/training.html