error from collapse function : TypeError: invalid value for Integer format about truvari HOT 2 CLOSED

Hello,

I believe I've seen this error before. When I've encountered it, there was a problem with the headers. The problem is that older versions of Truvari collapse (~v3.1?) added the annotation ##INFO=<ID=CollapseId,Number=1,Type=Integer, However, to make the annotation more informative for tracing chunks/pairs, it needed to be updated to a string ##INFO=<ID=CollapseId,Number=1,Type=String, (see wiki).

If my guess is correct, your input VCFs HG00096.vcf.gz, HG00171.vcf.gz, and HG00512.vcf.gz already have the CollapseId defined in the header as Integer type and pysam won't overwrite existing header lines.

Please try to remove CollapseId from your input VCF with:

bcftools annotate -x INFO/CollapseId  merge.vcf.gz -O z -o merge.fixed.vcf.gz

Then re-run collapse and let me know if that works.

Have a great day,
~/Adam

from truvari.

Thanks a lot! It works

from truvari.