marking variants in repeat regions
I'm hoping it's possible to mark variants in repetitive elements using variant filtration, so they can be selected out later. I've tried a few command variations, the most recent of which:
GenomeAnalysisTK -R local_reference/dm6.fa \ -T VariantFiltration \ -V my.vcf \ -filter "QD<5.0" -filterName "LowQD" \ -mask ../masking_intervals/dmel6_repMask.gatk.intervals -filterNotInMask -maskName "RepMask" \ -o my_marked.vcf
..fails with "No tribble type provided" for the intervals file.
Is this possible at all to do with VariantFiltration? Note that I'd rather mark the suspect variants for removal later, rather than just remove them altogether.
...actually in writing this, I just thought to create a new vcf of variants only in the intervals, and then use this vcf to screen out the original vcf..... Sound good ?