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phasing genotype

How can I "translate" the genotype of my vcf file in alleles? For example: 0|1 vs A|T

genotype
• 1,413 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by FRANCESCA • FRANCESCA

3 answers 

bcftools query -f'%REF|%ALT\n' in.vcf > output.txt

G|A
T|A
C|T
G|A
C|T
C|T
A|G
T|C
T|C
T|C
G|A
• 0 views • link
written by 4galaxy77 4galaxy77

If you want to reconstruct the haplotypes having a VCF with phased genotypes in place, I can recommend haplosaurus, developed by Ensembl.

• 0 views • link
written by iraun iraun 
bcftools query -f '%CHROM %POS %ID[ %TGT]\n' in.vcf
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

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