How to extract haplotype data from phased bcf files

Question

[Lynne-95]

Hello,

I have filtered/processed phased bcf files from wgs. I would like to extract the haplotype data per sample, so that I have a tab delim file which looks like this:

Sample	Chr	Pos	hap1	hap2
AW23	chr1	1234	A	C
AW45	chr1	1245	G	T

.

Currently I've tried to use bcftools as below to extract genotype data, but then that only gives the output in 0s/1s and not the alleles. I was also considering trying reading the data in Plink2 and converting to oxford gen format.

bcftools view -c1 -s ${sample} ${in_file}.bcf \
        | bcftools query -f '%CHROM\t%POS[\t%GT]\n' \
        | sed 's:|:\t:g' - > ${sample}_hap.txt

.

Any ideas of how best to go about this?
Ty for any help in advance! + apologies if I've missed this in the manual somewhere.

Answer 1

[Pierre Lindenbaum]

use %TGT (translated genotype)

$ bcftools query -f '[%CHROM %POS %TGT\n]' 

[Lynne-95]

Thanks that worked perfectly!