Genotype Calling

Question

[aditi.qamra]

Hi,

i wanted to create a vcf file with the genotype of my sample. I am a little confused on how to extract that information ( if we can at all) from output files of mutation callers like Varscan2 or GATK haplotype caller ?

Answer 1

[donfreed]

The default output of GATK's HaplotypeCaller is a VCF.

It looks like VarScan2 outputs a VCF with the --output-vcf switch.