Comments (1)
ACEnglish
commented on May 27, 2024
This is happening because your VCF does not define the length in the header's definition of the contigs. Apparently it's not required by the VCF format specification, but Truvari needs it to create the default interval trees.
This can be fixed by editing your VCF's header with something like
##contig=<ID=chr1,Description=chromosome chr1,length=1234567890>
It may also be possible for you to provide a --includebed with all the chromosomes you wish to process. e.g.
chr1 0 1234567890
....
from truvari.
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