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if initial base of one variant is deleted by another, SMaSH fails to rescue #9

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jn80842 opened this issue May 20, 2014 · 0 comments

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jn80842 commented May 20, 2014

Insertion/deletions are represented in VCF format by an initial unchanged base followed by the bases to be added/removed. If that leading reference base is deleted by another variant, SMaSH won't evaluate that sequence correctly. The example shows two underlying sequences that should be the same, but don't evaluate as equivalent.

true.vcf

fileformat=VCFv4.1

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

chr13 86457911 . C G 20 PASS . GT 0/1
chr13 86457912 . TCCCC T 20 PASS . GT 0/1
chr13 86457916 . C CGAT 20 PASS . GT 0/1
chr17 63587129 . CCACA C 20 PASS . GT 0/1
chr17 63587133 . A ATG 20 PASS . GT 0/1

pred.vcf

fileformat=VCFv4.1

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878

chr13 86457911 . CTCCCC GTGAT 20 PASS . GT 1|0
chr17 63587130 . CACA TG 20 PASS . GT 1|0

jn80842 pushed a commit that referenced this issue Aug 6, 2014
pull in julie's latest changes
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