vcf2phylip icon indicating copy to clipboard operation
vcf2phylip copied to clipboard

Published 20 hours ago • verified publisher icon edgardomortiz

output for phased data

Open erikenbody opened this issue 3 years ago • 5 comments

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

erikenbody avatar Feb 24 '21 03:02 erikenbody

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

edgardomortiz avatar Feb 25 '21 09:02 edgardomortiz

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

matthewglasenapp avatar Aug 12 '21 21:08 matthewglasenapp

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

sofiatorreggiani avatar Feb 01 '22 17:02 sofiatorreggiani

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

bbandriola avatar Jul 25 '23 15:07 bbandriola

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.

chrchang avatar Sep 22 '23 23:09 chrchang