Following a previous post: BaseRecalibrator - no suitable codecs – GATK (broadinstitute.org)
I think that my problem lies on not choosing correctly the reference genome for my samples. I was given the samples without the reference genome FASTA file. My samples come from the 1000 Genome Project Phase 3. With a bit of research I discovered that the reference genome for these samples were the hs375d reference genome.
Is this reference genome available in the GATK-bundle (FASTA and VCFs with known variants) ?
Please sign in to leave a comment.