Calling CNV using bcftools
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!
1 answer
$ 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.
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Pierre Lindenbaum
I recommend this training to understand more: https://support.illumina.com/array/array_software/genomestudio/training.html
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