How to filter out mixed SNP/spanning deletion variants?

[WimSpee]

Hi,

I used to use this bcftools command to select for pure SNP variants (i.e. SNP only, also no mixed variants.)

bcftools view --exclude-types indels,mnps,other

When filtering VCF files produced by GATK4 this command does not filter out SNP+spanning deletion variants.
https://software.broadinstitute.org/gatk/documentation/article.php?id=6926

Chr_14  32413   .       C       T,* 
Chr_14  105801  .       C      *,G

Also exluding bnd type variants does not help.
bcftools view --exclude-types indels,mnps,other,bnd

Is there another way to also exclude this type of mixed variants? Or shouldn't this type of variants fall under the existing indels type?

Thank you.

[pd3]

Hi,

just pushed a commit db2e2b6 which allows to filter these records using

-e'ALT="*" || type!="snp"'

As described in the commit message, this should be changed in htslib eventually.

[WimSpee]

Thank you.