Decoy sequence for human reference GRCh38 assembly

1

Entering edit mode

3.4 years ago

priya.bmg ▴ 60

Hello

I am trying to understand the GATK pipeline. Now I am stuck in the base recalibration step. There seems to be issue in the reference sequence, no overlapping contigs. Can anyone suggest a site from where I can download the human reference genome assembly GRCh38 with decoy sequence?.

Thanks

Priya

reference genome Decoy assembly Human • 1.7k views

ADD COMMENT • link updated 3.4 years ago by Tm ★ 1.1k • written 3.4 years ago by priya.bmg ▴ 60

1

Entering edit mode

This error has been addressed number of times. Please refer COSMIC vcf file compatibility for Mutect2 and GATK BaseRecalibrator - Input files knownSites and reference have incompatible contigs post.

ADD REPLY • link updated 3.4 years ago by GenoMax 148k • written 3.4 years ago by Tm ★ 1.1k

2

Entering edit mode

Tm : Biostars code understands biostars links. You can can simply include links in your post and they will be rendered with the post title. I have made the change this time.