Hi GATK Team,

I'd like to know if it possible to restrict the output to within a specific interval? I am running ApplyVQSR and supplying an interval file with the interval

chr1 111057913 117227796 + .

using the -L argument. The resulting output has a variant 

chr1 111057911 . TCATC T .

This will cause an issue if I do the merging (with other files) without any sanity checks and try to sort the merged file if the file before this one has the same variant. 

I am trying to avoid doing any sanity checks during the merging or sorting after merging as they can be expensive. Is there an argument I can use to make sure the output only contains variants within a specific interval? In the case above, the output file wouldn't have the following variant

chr1 111057911 . TCATC T .

since the file before this one will have the same variant (chr1:104888029-111057912 interval)

UPDATE

As a workaround, I've tried SelectVariants and supplying the same interval_list file used to create the VCF but somehow the variant still ends up in the final VCF. Is there an argument I am missing?

gatk SelectVariants \\
  -V input.vcf.gz \\
  -L scattered.interval_list \\
  -O output.vcf.gz

I can achieve the desired result with bcftools the following way:

bcftools view -t chr1:111057913-117227796 input.vcf.gz --output output.vcf.gz --output-type z

UPDATE 2

The ref allele is in the specified interval, which makes sense why the variant is not removed. It would've been great though to have a feature that allowed one to choose how "strict", with regards to the position, the selection/filtering should be.

This issue can be marked as fixed. Thanks