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