Variant Calling with Vartrix: Warning with VCF and Error with FASTA
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6 weeks ago
d • 0

I am getting the following warnings/errors when running my vcf file through Vartrix. I am using the hg38 reference as my fasta file.

[W::vcf_parse] Contig '' is not defined in the header. (Quick workaround: index the file with tabix.)
02:20:04 [ERROR] Sequence  not seen in FASTA

I have tried using tabix to index the bgzipped file (after sorting by position) and get the following error as well:

Failed to parse TBX_VCF, was wrong -p [type] used?
The offending line was: ""

Any tips?

vcf vartrix fasta • 204 views
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Try bcftools index instead of tabix.

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I got a similar error, which was:

[E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?
The offending line was: ""
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