Variant Calling with Vartrix: Warning with VCF and Error with FASTA
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?
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Try
bcftools indexinstead oftabix.I got a similar error, which was: