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sites-a.vcf.gz contains a variant with AF = 0.0099
The following command creates a Segmentation fault:
bcftools isec -p test -i'AF>0.09' sites-a.vcf.gz sites-b.vcf.gz
This command does not create a Segmentation fault (note that all variants from the datasets are now included):
bcftools isec -p test -i'AF>0.009' sites-a.vcf.gz sites-b.vcf.gz
You can create other scenarios with -e instead of -i creating Segmentation faults. Similar filtering works with other commands like bcftools view etc. Attached are sample files.
I was able to work around the issue with merging and filtering files, but it would be nice if the filter option in the isec command would work.
bcftools 1.14
sites-a.vcf.gz
contains a variant withAF = 0.0099
The following command creates a Segmentation fault:
This command does not create a Segmentation fault (note that all variants from the datasets are now included):
You can create other scenarios with
-e
instead of-i
creating Segmentation faults. Similar filtering works with other commands likebcftools view
etc. Attached are sample files.I was able to work around the issue with merging and filtering files, but it would be nice if the filter option in the
isec
command would work.filter.zip
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