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SMaSH does not evaluate compound het variants correctly #8

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jn80842 opened this issue May 19, 2014 · 0 comments
Open

SMaSH does not evaluate compound het variants correctly #8

jn80842 opened this issue May 19, 2014 · 0 comments

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@jn80842
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jn80842 commented May 19, 2014

SMaSH doesn't evaluate compound heterozygous variants correctly (phased or unphased).

true.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

chr13 20332447 . C T 20 PASS . GT 0/1
chr13 20332452 . CA C 20 PASS . GT 0/1

pred.vcf

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

chr13 20332447 . CGTCTCA TGTCTCA,CGTCTC 20 PASS . GT 1/2

Evaluates to two false negatives and one false positive.
jn80842 pushed a commit that referenced this issue Aug 6, 2014
@kwestbrooks
Merge pull request #8 from amplab/master
ca66a3a 
get known fp mode to work
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