Invalid argument and BCF warning about truvari HOT 2 CLOSED

Hello,

The problem is the INFO/SEQ field. Some insertions seem to be too long for pysam/htslib to write. Using INFO/SEQ is surprisingly common, but Truvari expects insertion sequences to be inside the ALT column, which - to me - seems like a more logical place for the sequence. Please try to alter your VCFs with the below script (note I made this fast, so it's provided without warranty)

import sys
import pysam

in_vcf = pysam.VariantFile(sys.argv[1])
out_vcf = pysam.VariantFile(sys.argv[2], 'w', header=in_vcf.header)

for entry in in_vcf:
    entry.alts = (entry.info["SEQ"])
    del(entry.info["SEQ"])
    out_vcf.write(entry)

from truvari.

No problem, the pipeline I'm using can write both full ALTs and symbolic alts. Works with the sequence in ALT, thanks!

For the code above, wouldn't you need to add the reference base to the ALT column to make the correct ALT? Mentioning it in case someone finds and uses it.

Thanks for the quick reply!

from truvari.