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hall-lab / speedseq

A flexible framework for rapid genome analysis and interpretation
MIT License
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about using GRCH38 #92

Open liminghao663 opened 8 years ago

liminghao663 commented 8 years ago

In your instruction:

"For human genome alignment using the GRCh37 build, we recommend using the annotations/ceph18.b37.include.2014-01-15.bed windows to parallelize variant calling (speedseq var and speedseq somatic). "

But I want to using GRCH38 ref genome to do mapping, what should I do? which bed windows should I choice?

Thanks for your help

jgbaum commented 7 years ago

Any update on this? We are interested in using GRCh38 as well, as I imagine are others. If there is no annotation file provided, are there instructions on how the community can create one? That would be much appreciated.

Thanks,

Jason

dantaki commented 7 years ago

To add... I've attempted to genotype SVs with speedseq sv -gusing hg38 aligned genomes. I used an exclusion file that contained gaps, centromeres, and segmental duplications for hg38 and SVTyper fails to genotype SVs. I've also lifted-over the hg19 exclusion file to hg38 and SVTyper still fails to genotype SVs.

crazyhottommy commented 4 years ago

any update on this? or as @jgbaum mentioned, how to create such a file for hg38? thanks!

crazyhottommy commented 4 years ago

FYI, there is one can download from GATK https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/