sigven / vcf2tsvpy Goto Github PK

Hi, I am running vcf2tsv on an annotated VCF file, and getting this error:

> python3 vcf2tsv.py myhg38.hg38_multianno.vcf myhg38.hg38_multianno.tab
[W::vcf_parse] INFO '.' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'REVEL_rankscor' is not defined in the header, assuming Type=String
Segmentation fault

How can I resolve this? Any help would be greatly appreciated, thanks!

I have run vct2tsvpy with default arguments i.e. only required arguments with the following command:

vcf2tsvpy --input_vcf {in_vcf} --out_tsv {out_tsv} --skip_info_data

I have noticed, however, that some entries from the vcf, which have a PASS value under FILTER column were excluded from the output tsv file.

For example, the entry below is present on the vcf:

1       776546  rs12124819      A       G       .       PASS    .       GT:GQ:BAF:LRR   ./.:0:0.590754:0.0825162

but it is not present in the output tsv file, unless I pass the --keep_rejected_calls, in which case, the tsv file is complete.

Below is a vimdiff screenshot, the left-hand side with --keep_rejected_calls, right-hand side only with required arguments.

Is this the expected behaviour? How come not passing --keep_rejected_calls excludes calls that have a PASS under FILTER?

Thanks in advance