Error in VCF files
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In the generated VCF files the columns headers are seperated by spaces instead of tabs. This inconsistency causes BCFtools to be unable to parse the header:
bcftools view PC1-10.vcf
[W::bcf_hdr_parse] Could not parse header line: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE
[E::bcf_hdr_parse] Could not parse the header, sample line not found
Failed to open PC1-10.vcf: could not parse header
Hi @jakob1482, thanks for letting us know!
We have fixed this in the latest commit. You may 'git pull' the latest commit or replace 'predict.py' in VarNet's root directory with the updated version here: https://github.com/skandlab/VarNet/blob/e385c4f12b9f2baf9359cffde78898ac21c3272e/predict.py
To re-generate the above VCF file, simply delete the VCF file in the output directory and re-run the predict.py step. Let us know if there are any further issues.