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edgardomortiz / vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
GNU General Public License v3.0
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Coordinates of alignment sites #36

Closed matthewglasenapp closed 3 years ago

matthewglasenapp commented 3 years ago

Thank you for such a useful tool. Is it be possible to extract the coordinates for the sites included in the alignment?

edgardomortiz commented 3 years ago

It didn't before but it can now! Just re-clone the repository for version 2.7, you can add the option -w or --write-used-sites to your commands to create a tab-separated file of the coordinates of the used sites and the number of samples on each site.

Edgardo

matthewglasenapp commented 3 years ago

Incredible! Thanks so much! Worked perfectly.