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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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output for phased data #29

Open erikenbody opened 3 years ago

erikenbody commented 3 years ago

Hi there,

Thank you for making this super useful tool! Issue #23 was a really helpful improvement for utilizing heterozygous sites. I was wondering if it would be feasible to include an option for an output file that is two alignments per diploid individual? E.g.

Ind1_A ATGCAA Ind1_B GTACCG

This would provide a reasonable alternative to discarding het sites or selecting them randomly when the data is phased confidently.

Thank you! Erik

edgardomortiz commented 3 years ago

I have been recently working with phased genotypes. I will give it a try, but I am really busy at the moment, I will work on that perhaps on the weekend.

Edgardo

matthewglasenapp commented 3 years ago

Was this added as a feature? This would be very useful to me as well.

sofiatorreggiani commented 2 years ago

I would be very interested in this as well. Thank you! Sofia

bbandriola commented 1 year ago

Hi there, Is there any update about the phasing option?

chrchang commented 1 year ago

plink2 (https://github.com/chrchang/plink-ng ; will post precompiled binaries to https://www.cog-genomics.org/plink/2.0/ after I test for a few more hours) now supports this for diploid data. Sample usage:

plink2 --vcf [vcf filename, could be gzipped] --geno [max missing-call rate] --snps-only --export phylip-phased used-sites --out [output filename prefix]

Replace "phylip-phased" with "phylip" for regular phylip output.