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human_chm13v2p0_maskedY_rCRS

About

This is a modified "analysis set" version of the human CHM13 v2.0 assembly, GCA_009914755.4.

Details

  • This is our recommended CHM13 reference for typical variant calling applications in human samples.
  • chromosome names are chr1, chr2, ..., chrM, chrX, chrY
  • the autosomes and chrX are assembled from the CHM13 cell line
  • chrY is assembled from sample HG002/NA24385
  • pseudoautosomal regions (PAR) are masked to N on chrY
  • mitochondrial sequence is replaced with rCRS (NC_012920.1)

Annotations

PAR intervals:

chrX    0           2394410     PAR1
chrX    153925834   154259566   PAR2
chrY    0           2458320     PAR1
chrY    62122809    62460029    PAR2

Annotations are available for pbsv. See the README for details.

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