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Question: Haplotype analysis from phased vcf
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Hi,

I want to ask that how can I perform haplotype analysis from phased vcf. I have vcf in this format.

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  S1     S2      S3      S4     S5     S6
10      94870   rs123        A       G       30      PASS    AN=20;AC=11     GT      ./.     ./.     ./.     ./.     ./.     ./.     1|0     ./.     ./.
10      94872   rs456        A       C       30      PASS    AN=20;AC=11     GT      ./.     ./.     ./.     ./.     ./.     ./.     1|0     ./.     ./.
10      95074   rs345        G       A       30      PASS    AN=22;AC=13     GT      0|1     1|0     ./.     ./.     ./.     ./.     1|0     ./.     ./.
10      95096   rs234      A       G       30      PASS    AN=26;AC=19     GT      1|0     1|1     1|1     0|1     1|1     0|1     ./.     1|1     ./.

I want pharmgkb haplotype table this like.

LOCATION    ALLELE  REFERENCE ALLELE
rs2230037   A   G
rs5030868   A   G

Is there any way to do this.

ADD COMMENTlink 17 months ago BAGeno • 130
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0

from your input and output, you just need cut -f3-5 and I don't see how it's related to 'phasing'

ADD REPLYlink 17 months ago
Pierre Lindenbaum
120k

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