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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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Jasmine produces invalid VCF #59

Open zeeev opened 5 months ago

zeeev commented 5 months ago

bcftools sort exits with the error below. I tested the same sort on all the input files eliminating the possibility that the inputs are problematic.

  1. Jasmine is not constructing a valid header

    [W::vcf_parse_info] INFO 'SVANN' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'DP' at chr1:669651 is not defined in the header, assuming Type=String

  2. Jasmine appears to be generating SVs that have invalid coordinates (I'm guessing off by one for insertions)

[W::vcf_parse_info] INFO/END=146984883 is smaller than POS at chr1:146991183

Full error:

[W::vcf_parse_info] INFO/END=146984883 is smaller than POS at chr1:146991183
[W::vcf_parse_info] INFO 'SVANN' is not defined in the header, assuming Type=String
[W::vcf_parse_format] FORMAT 'DP' at chr1:669651 is not defined in the header, assuming Type=String
Error encountered while parsing the input at chr1:669651
Cleaning
tnguyengel commented 3 weeks ago

Also getting this error. Jasmine v1.1.5.