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If you have symbolic variants with the same chrom/pos/ref/alt but different SVLEN, they are treated as identical, meaning you silently drop symbolic variants
Example VCF:
##fileformat=VCFv4.1
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
#CHROM POS ID REF ALT QUAL FILTER INFO
NC_000012.11 88520131 23651 C <DEL> . . SVLEN=-1000;SVTYPE=DEL
NC_000012.11 88520131 24042 C <DEL> . . SVLEN=-2000;SVTYPE=DEL
NC_000012.11 88520131 24043 C <DEL> . . SVLEN=-3000;SVTYPE=DEL
These are different variants (1k, 2k, 3k deletions) and are not unique.
Ideally, vt would take into account SVLEN
At the least - if you see a symbolic alt, you should perhaps write a warning to STDERR saying that symbolic variants are not treated correctly, and will be removed
The text was updated successfully, but these errors were encountered:
If you have symbolic variants with the same chrom/pos/ref/alt but different SVLEN, they are treated as identical, meaning you silently drop symbolic variants
Example VCF:
These are different variants (1k, 2k, 3k deletions) and are not unique.
Ideally, vt would take into account SVLEN
At the least - if you see a symbolic alt, you should perhaps write a warning to STDERR saying that symbolic variants are not treated correctly, and will be removed
The text was updated successfully, but these errors were encountered: