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vcf2loc 0.1.0
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@tomkurowski tomkurowski released this 18 Aug 00:54
· 21 commits to master since this release
0.1.0
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Initial release of my GBS-based VCF to JoinMap loc file conversion script.

  • Requires Python 3.7 or newer (standard library only). It may also work with Python 3.6 with a dataclasses backport.
  • Only the CP population type supported.
  • Multiallelic sites (i.e. more than one alternate non-reference allele) are ignored.
  • Genotype calls in the VCF files should be unphased.
  • The first entry in the VCF ID field is used as the marker name (the TASSEL 5 GBSv2 pipeline creates these). If there are no IDs, the CHROM and POS fields are used to create a marker name.
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