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Advanced Filtering of SNPS
I'm looking for pairs of nearby SNPs with the following properties:
- of two given samples, one is HOM_REF at the locus while the other is HOM_VAR
- the locus is close to another with property 1. (say 50bp, but should be configuarable)
Any ideas how I could filter a VCF to obtain such a reduced subset? (I could write a walker, but was hoping to get some of the work done by an existing one)