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AndersenLab / VCF-kit

VCF-kit: Assorted utilities for the variant call format
http://www.andersenlab.org
MIT License
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VK does not work with plink outputed VCF because the AC is empty #12

Closed andreyurch closed 6 years ago

andreyurch commented 6 years ago

vk tajima --no-header --extra 100000 50000 plink.vcf Traceback (most recent call last): File "/usr/local/lib/python2.7/site-packages/vcfkit/tajima.py", line 146, in main() File "/usr/local/lib/python2.7/site-packages/vcfkit/tajima.py", line 142, in main for i in tajima(args[""]).calc_tajima(wz, sz, args["--sliding"], extra=args["--extra"]): File "/usr/local/lib/python2.7/site-packages/vcfkit/tajima.py", line 80, in calc_tajima AC = variant.INFO["AC"] File "cyvcf2/cyvcf2.pyx", line 1880, in cyvcf2.cyvcf2.INFO.getitem (cyvcf2/cyvcf2.c:36641) KeyError: 'AC'

fileformat=VCFv4.2

fileDate=20171123

source=PLINKv1.90

contig=

INFO=

FORMAT=

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT t1 t2 t3

24 430241 24_430241 G A . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 1 24 478701 24_478701 A G . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 1/1 1/1 0/1 . 24 576821 24_576821 A G . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 . 24 587710 24_587710 G A . . PR GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/1 0/1 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0 24 602258 24_602258 G A . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 1/1 0/1 0/1 0/0 1/1 1/1 1/1 1/1 . 24 632760 24_632760 G A . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 . 24 653401 24_653401 G A . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 0/1 1/1 1/1 . 24 679380 24_679380 A G . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/0 0/1 0/1 0/0 1/1 0/1 1/1 0/1 0 24 706868 24_706868 G A . . PR GT 0/0 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0 24 734205 24_734205 G A . . PR GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 . 24 757597 24_757597 G A . . PR GT 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0 24 770828 24_770828 A G . . PR GT 0/0 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/1 0/0 0/1 0 24 785766 24_785766 G A . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 0/0 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 . 24 797195 24_797195 A G . . PR GT 0/0 0/1 1/1 0/1 0/0 0/0 0/1 1/1 0/0 0/0 0/1 0/1 0/1 0/1 1/1 0/0 0/0 0/0 0/1 0 24 823211 24_823211 A G . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 . 24 832216 24_832216 G A . . PR GT 1/1 0/1 0/0 0/1 1/1 1/1 0/1 1/1 1/1 1/1 0/1 0/1 0/1 0/1 0/0 1/1 1/1 1/1 0/1 .

danielecook commented 6 years ago

Run your vcf through vcffixup, a part of vcflib, first.

# install vcffixup with brew install vcflib on mac os
bcftools view <vcf> | vcffixup - | vk tajima ...
andreyurch commented 6 years ago

Thanks! It works in this way!