Using sniffles 2.4 in merge mode on chm13 produced an invalid variant.
This isn't a huge problem because most vcf parsers can handle the error plus SVs at the beginning of chromosomes should be a rare occurrence(?). But I just wanted to report it.
Error:
[W::vcf_parse_info] INFO/END=0 is smaller than POS at chr11:1
Offending Line:
chr11 1 Sniffles2.INS.8M0 t tCCCAACCCCACCCGAACTCCGAACCCCAACTCCGAACCCCAACTCGAACCCGAACCCTAACCCGAACCTTGAATTCGAACT50 PASS PRECISE;SVTYPE=INS;SVLEN=87;END=0;SUPPORT=3;COVERAGE=10,13,14,15,23;STRAND=+-;AC=22;STDEV_LEN=10.746;STDEV_POS=393.116;SUPP_VEC=0000000000000000000010000000000000000000000000000000000000000000000000000010000000000000010000100000000000000000000000000000000000001000000000010000000000000000001000000100001000000000000000000010000000000100100000000000000000000000000000000000000000000000000000000000000000000000010000000000000010000000000000000000000011000000000000000000000000000000000000010000010000000000000000000000100100000000100000000000000000000000000010000000000000000000000000000100000000000000000000000000011000000100000000000000001000000000010000000000000000100000000000000000000101000000100000010000000000000000000000000000010000000000000000000000000000000000000000000000001000000000000000000000000000000000000000000000011000000000000001000000000000001001000000000001000000000000000000000000000000000000000000000000000000000000000000000100000000000000000000000000000000000000000000000001000101000000000000010000000000000000000000000000000000000000000000000000000000000000000100000001010000000000001000000000000000000000000100000000000000000000000001001100000000000000010000000100000000000000100000000000000 GT:GQ:DR:DV:ID 0/0:0:25:0:NULL
Using sniffles 2.4 in merge mode on chm13 produced an invalid variant.
This isn't a huge problem because most vcf parsers can handle the error plus SVs at the beginning of chromosomes should be a rare occurrence(?). But I just wanted to report it.