I have managed to generate vcf files by using bwa + PiCard + GATK pipeline, and would like to use ANNOVAR to do the variant calling. I checked the vcf content output from GATK, and think it is not ready for feeding into ANNOVAR. I was wondering if there's any handy tool to prepare the GATK vcf files for ANNOVAR? thanks for reply
From the ANNOVAR manual:
perl convert2annovar.pl infile.vcf -format vcf4 > outfile
As an aside, I think you are slightly confused when you say use ANNOVAR to do "variant calling". What you have in your vcf file are variants that were called using GATK. ANNOVAR does ANNOtation of VARiants by either locating interrupted or closest genomic features (genes, transcription factors, etc.) or filtering the variants based on another set of variant genotypes you supply.