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pave v1.2
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@charlesshale charlesshale released this 09 Apr 09:34
· 5668 commits to master since this release
pave-v1.2
9ff7ba3

Functional:

  • optionally annotate with blacklistings (BED and VCF), mappability and Clinvar significance
  • annotate and filter with PON
  • annotate and filter with Gnomad population frequency
  • added optional read and write pass filter

Bugs:

  • fixed PAVE_TI VCF item count to unbounded
  • prevent phasing without multiple INDELs or INDEL+SNV

Config:

  • read_pass_only / write_pass_only
  • pon_file & pon_filters - see read-me for format and details
  • pon_artefact_file - use for GRCh38 artefacts for tumor-only target-regions
  • gnomad_freq_dir / gnomad_freq_file + gnomad_load_chr_on_demand - see read-me for details
  • gnomad_pon_filter (default: 0.00015)
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