Genotype Calling
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 ?
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aditi.qamra
1 answer
The default output of GATK's HaplotypeCaller is a VCF.
It looks like VarScan2 outputs a VCF with the --output-vcf switch.
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