Question

Genomes in a Bottle for GRCh38

2

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8.7 years ago

mark.fleharty ▴ 40

Is there a VCF file containing the GIAB sites available that are mapped to assembly GRCh38?

GIAB Genomes in a bottle GRCh38 • 2.5k views

ADD COMMENT • link updated 8.7 years ago by Brad Chapman 9.7k • written 8.7 years ago by mark.fleharty ▴ 40

score 0 · Answer 1 · 2015-08-11

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8.7 years ago

SteveL ▴ 90

Not yet I don't believe, as they are still completing analyses on GRCh37 but they are putting together materials for GRCh37, so hopefully sometime in the next few months.

ADD COMMENT • link 8.7 years ago by SteveL ▴ 90

score 0 · Answer 2 · 2015-08-11

Steve is right that the Genome in a Bottle group is still working on a native 38 build of the reference. In the short term, we've been doing work on providing a Remapped/Crossmapped version that converts the 37 reference to 38 coordinates. This isn't finished as I'm not happy with the Remapping of SNPs, but it's useful right now where since are no other existing resources for validation on 38 that I know of. Here is the repository with details and scripts:

https://github.com/hbc/giab_remap_38

The validations:

http://imgur.com/a/2Ezon

and the files:

http://biodata.s3-website-us-east-1.amazonaws.com/giab_hg38_remap/