Question: Why VarScan cannot call variants which appear in 1000genome
gravatar for sxl919
3.8 years ago by
United States
sxl91910 wrote:


I am using VarScan for variant calling and I use the bam files from 1000genome as control for my project. I run the bam file through VarScan using default setting and then annotate the vcf using Annovar. However, when I try to compare the vcf generated from VarScan and the vcf from 1000 genome, there are some variants which VarScan hasn't called. For example, for SNP rs10000057 is called in the 1000 genome vcf files but it didn't get any calls in the VarScan generated vcf files. Has anyone experience the same situation as I do? Can anyone explain why?

Thank you 

1000genome varscan • 1.2k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by sxl91910

What do you mean by VarScan didn't call ? Are they truly present in your bam file (IGV lookup) ?

ADD REPLYlink written 3.8 years ago by poisonAlien2.7k

Thanks for your comment. I did look at the IGV and the variant is present. However, I was doing variant call individually so I do think that the variant will show up if I do a joint calling.

ADD REPLYlink written 3.8 years ago by sxl91910

hopefully joint call will help (going to know whether VarScan call that position tomorrow)

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by sxl91910
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