Decoy sequence for human reference GRCh38 assembly

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

• 2,431 views • link

updated 5.0 years ago by Tm

• written 5.0 years ago by priya.bmg •

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.

• 0 views • link

updated 5.0 years ago by GenoMax

• written 5.0 years ago by Tm

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.

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written 5.0 years ago by GenoMax

Ok got it. Thank you.

• 0 views • link

written 5.0 years ago by Tm

0 answers

No answers yet.

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