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SelectVariants and large deletions
I am using BWA/GATK Haplotype caller on core exom sequences.
In my pipeline I use an extended (250bp padding around exons for indels/50bp for SNPS) bed interval file to identify variants.
Following that, I use SelectVariants to filter out core variations with narrower bed coordinates (50bp padding for indels, 10bp for SNPs).
Everything is fine with SNPs, and insertions, however in case of large deletions SelectVariant is filtering out large deletions that are started outside of the core bed coordinates, even though the end of the deletion overlaps the narrower bed coordinates.
To visualise the problem I am attaching an IGV view, where the extended list contains the large deletion, however in the core list it is absent.
Is there any way to fix this issue? Calling the variants twice with different bed coordinates would require unnecessary computation power.