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genome-in-a-bottle / giab_data_indexes

This repository contains data indexes from NIST's Genome in a Bottle project.
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Data descriptions for newer data #6

Closed anands-repo closed 4 years ago

anands-repo commented 4 years ago

Hi,

Data descriptions for some of the raw data is greatly appreciated. Specifically, I am looking for information regarding

  1. Alignment method/any error correction used over raw subreads for alignments in ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/Baylor_NGMLR_bam_GRCh37/
  2. Description of sequencing method used for ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NA12878_PacBio_MtSinai/. Is it the same as that for HG002 (which is described in the original publication - https://www.nature.com/articles/sdata201625)?

Thanks!

fritzsedlazeck commented 4 years ago

Hi, for point 1: no raw read correction was done.

point2: yes it is. Its an older set of Pacbio sequencing run I think even on RS2 from back then.

Thanks Fritz

anands-repo commented 4 years ago

Thanks!

By the way, is a new release imminent? If so, broadly, what may be expected from it, may I ask?

fritzsedlazeck commented 4 years ago

You mean for the SV calls ? We do have the SNV release under review right now. SV calls is not a new release expected. Thanks Fritz