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Bug: missing headers #51

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fgvieira opened this issue May 6, 2022 · 0 comments
Open

Bug: missing headers #51

fgvieira opened this issue May 6, 2022 · 0 comments

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@fgvieira
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fgvieira commented May 6, 2022

Running svdb v2.6.1 as:

svdb --merge --vcf cnvnat delly lumpy manta --pass_only --no_intra --no_var --overlap 0.1 --bnd_distance 1000

and passing the output through bcftools, I am getting some missing headers:

[W::bcf_hrec_check] Invalid tag name: "cnvnat_INFO"
[W::bcf_hrec_check] Invalid tag name: "cnvnat_SAMPLE"
[W::bcf_hrec_check] Invalid tag name: "cnvnat_CHROM"
[W::bcf_hrec_check] Invalid tag name: "cnvnat_POS"
[W::bcf_hrec_check] Invalid tag name: "cnvnat_QUAL"
[W::bcf_hrec_check] Invalid tag name: "cnvnat_FILTERS"
[W::bcf_hrec_check] Invalid tag name: "delly_INFO"
[W::bcf_hrec_check] Invalid tag name: "delly_SAMPLE"
[W::bcf_hrec_check] Invalid tag name: "delly_CHROM"
[W::bcf_hrec_check] Invalid tag name: "delly_POS"
[W::bcf_hrec_check] Invalid tag name: "delly_QUAL"
[W::bcf_hrec_check] Invalid tag name: "delly_FILTERS"
[W::bcf_hrec_check] Invalid tag name: "lumpy_INFO"
[W::bcf_hrec_check] Invalid tag name: "lumpy_SAMPLE"
[W::bcf_hrec_check] Invalid tag name: "lumpy_CHROM"
[W::bcf_hrec_check] Invalid tag name: "lumpy_POS"
[W::bcf_hrec_check] Invalid tag name: "lumpy_QUAL"
[W::bcf_hrec_check] Invalid tag name: "lumpy_FILTERS"
[W::bcf_hrec_check] Invalid tag name: "manta_INFO"
[W::bcf_hrec_check] Invalid tag name: "manta_SAMPLE"
[W::bcf_hrec_check] Invalid tag name: "manta_CHROM"
[W::bcf_hrec_check] Invalid tag name: "manta_POS"
[W::bcf_hrec_check] Invalid tag name: "manta_QUAL"
[W::bcf_hrec_check] Invalid tag name: "manta_FILTERS"

If I also include the option --notag, svdb_origin is not included in the header, even though it is in the VCF file.

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