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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
The text was updated successfully, but these errors were encountered:
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.
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
The text was updated successfully, but these errors were encountered: