SNP discovery form replicated files of 2 varities

Question

[sultan0083]

Hi, I have got 6VCF files from 6 RNA-Seq libraries (2 varieties, each with 3 replications), I was wondering how to identify SNP between the two varieties? should i merge each of the 3 VCF files into 1?

Answer 1

[shubhra.bhattacharya]

Hi! Since you have the vcf file already it is implied you have already performed variant calling. What do then mean by identify variants because .vcf file has variants itself.

However if you have the bam file have you decided which tool and utility to use for variant calling? In case, you're using GATK this link maybe helpful: https://gatkforums.broadinstitute.org/gatk/discussion/5894/variant-calling-with-biological-replicate