Question

phasing genotype

0

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18 months ago

FRANCESCA ▴ 10

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

genotype • 682 views

ADD COMMENT • link updated 18 months ago by Pierre Lindenbaum 161k • written 18 months ago by FRANCESCA ▴ 10

score 1 · Answer 1 · 2022-10-20

1

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18 months ago

4galaxy77 2.8k

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

ADD COMMENT • link 18 months ago by 4galaxy77 2.8k

score 1 · Answer 2 · 2022-10-20

1

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18 months ago

iraun 6.2k

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

ADD COMMENT • link 18 months ago by iraun 6.2k

score 1 · Answer 3 · 2022-10-20

1

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18 months ago

Pierre Lindenbaum 161k

bcftools query -f '%CHROM %POS %ID[ %TGT]\n' in.vcf

ADD COMMENT • link 18 months ago by Pierre Lindenbaum 161k