vcf2loc 0.4.0

Changelog

• Natural sorting of individuals by name in the output is now available through the --natural-sort flag.
• Bug fix: Missing values ('.') are now allowed for DP and GQ in genotype fields.

vcf2loc 0.3.0

Changelog

• Providing the -b / --parent-b argument is now optional for population types other than CP (i.e. for F2 and RIx). Unless all of the genotype calls made for the population were identical to the homozygous parent A (in which case the site is not considered a valid marker site and is ignored), the alternative allele in the population is treated as if it was known to come from a homozygous / haploid parent B.

vcf2loc 0.2.0

Changelog

• Added experimental support for F2 and RIx population types.

vcf2loc 0.1.0

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.