output for phased data

[erikenbody]

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]

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]

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

[sofiatorreggiani]

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

[bbandriola]

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

[chrchang]

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.