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genome-in-a-bottle / giab_latest_release

This repository contains information about latest release from Genome in a Bottle project
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NA24385 high confidence SV hg38-based #9

Open MaestSi opened 5 years ago

MaestSi commented 5 years ago

Dear all, I would like to know if there is an "official" set of VCF and bed files for NA24385 (HG002) structural variants benchmarks, which has hg38 as a reference, similar to those reported in https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/ but lifted over. I have been trying to perform a Liftover with CrossMap (Picard gave issues), but I am not sure about the result of the conversion. Thanks in advance, Simone

jzook commented 3 years ago

Just revisiting this issue - liftover/remap of SVs and benchmark bed files is generally hard to do robustly, so we don't have a v0.6 equivalent benchmark on GRCh38. We do have a new SV benchmark for challenging medically relevant genes on GRCh38 and GRCh37, which is described in https://doi.org/10.1101/2021.06.07.444885. We plan to make future assembly-based benchmarks for chrX and for the whole genome on GRCh38 and GRCh37 over the next year or so.

gamzemdn commented 2 days ago

Hi! Any update on GRCH38 version of SV benchmark file?

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