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7.6 years ago
bioinforesearchquestions ▴ 370
I have a vcf file from GATK tool. I would like to filter and annotate the variants. Can any one suggest some tutorials or links which explain the parameters for filtering. Also I am looking for some and for annotating and filtering the variants.
as far as I know, GATK is only designed for diploid organisms...
I am using GATK's unified genotyper to call variants. I am using a haploid organism, and used the
-ploidyflag to indicate that to unified genotyper.
ok, I didn't know that option.