sbilge / nextflow-clinvap Goto Github PK

Hi there,

Maybe the vcf testdata could be gzipped and indexed with tabix to avoid the warnings below upon parsing the vcf file.

[W::vcf_parse] Contig 'chr1' is not defined in the header. (Quick workaround: index the file with tabix.)
[W::vcf_parse] Contig 'chr2' is not defined in the header. (Quick workaround: index the file with tabix.)
...

This could be done with the following command: bgzip out.vcf && tabix -p vcf out.vcf.gz (requires samtools).