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lgmgeo / AnnotSV

Annotation and Ranking of Structural Variation
GNU General Public License v3.0
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vcf errors #245

Open gevro opened 1 month ago

gevro commented 1 month ago

Hi, The final vcf is giving me these errors when I look at it with bcftools:

[W::bcf_hrec_check] Invalid tag name: "'SampleID'" [W::bcf_hrec_check] Invalid tag name: "Compound_htz(sample)" [W::bcf_hrec_check] Invalid tag name: "Count_hom(sample)" [W::bcf_hrec_check] Invalid tag name: "Count_htz(sample)" [W::bcf_hrec_check] Invalid tag name: "Count_htz/allHom(sample)" [W::bcf_hrec_check] Invalid tag name: "Count_htz/total(cohort)" [W::bcf_hrec_check] Invalid tag name: "Count_total(cohort)"

fileformat=VCFv4.2

[W::vcf_parse_format] FORMAT 'AD' at 1:90258 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'DP' at 1:90258 is not defined in the header, assuming Type=String [W::vcf_parse_format] FORMAT 'PS' at 1:136554 is not defined in the header, assuming Type=String

I suspect there are bugs in how annotSV is defining the vcf headers.

gevro commented 1 month ago

Note, if this is a variantconvert bug, maybe it would be best for annotsv to natively output to vcf? Since variantconvert bugs would take a long time to fix. Thanks