Decoy sequence for human reference GRCh38 assembly

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3.3 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 • 1.6k views

ADD COMMENT • link updated 3.3 years ago by Tm ★ 1.1k • written 3.3 years ago by priya.bmg ▴ 60

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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 3.3 years ago by GenoMax 147k • written 3.3 years ago by Tm ★ 1.1k

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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.