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human_hs37d5

About

This is an "analysis set" version of the human GRCh37 assembly, GCA_000001405.5.

Details

  • This is our recommended GRCh37/hg19 reference genome, but we recommend using GRCh38/hg38 instead. We have generated limited resources for this reference.
  • chromosome names are 1, 2, ..., M, X, Y
  • ALT contigs are excluded
  • pseudoautosomal regions (PAR) are masked to N on chromosome Y
  • mitochondrial sequence is replaced with rCRS (NC_012920.1)
  • Epstein-Barr virus (EBV) sequence is included as NC_007605
  • the concatenated decoy sequences (hs37d5cs) are included as hs37d5
  • we hard mask all non-ACGTN nucleotide codes to N

Annotations

PAR intervals:

X   60001       2699520     PAR1
X   154931044   155260560   PAR2
Y   10001       2649520     PAR1
Y   59034050    59363566    PAR2

Annotations are available for pbsv, HiFiCNV, and Paraphase. See the README for details.

DISCLAIMER

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