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fritzsedlazeck / Sniffles

Structural variation caller using third generation sequencing
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Invalid END position #497

Open ACEnglish opened 4 months ago

ACEnglish commented 4 months ago

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
hermannromanek commented 3 months ago

Hi @ACEnglish,

Which dataset did you see this on?

Thanks, Hermann

ACEnglish commented 3 months ago

This was in the 1kgp ONT data. Fritz has the snf files locally. https://www.biorxiv.org/content/10.1101/2024.04.18.590093v1.full.pdf

lfpaulin commented 1 month ago

@hermannromanek it looks like Sniffles is diminishing by 1 the end when outputting the END position and for INS its the same as start that when is 1 it becomes zero