Question: Haplotype analysis from phased vcf
0
gravatar for BAGeno
14 months ago by
BAGeno160
BAGeno160 wrote:

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.

phased haplotype vcf • 403 views
ADD COMMENTlink written 14 months ago by BAGeno160

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

ADD REPLYlink written 14 months ago by Pierre Lindenbaum124k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 889 users visited in the last hour