removing SNPs by indel boundaries ?

Will_GilksWill_Gilks University of Sussex, UKMember ✭✭

Is removing SNPs close to indel boundaries still recommended - having performed GATK local realignment and HaplotypeCaller - or do these processes mean that SNPs near indels are now called more accurately? If boundary SNPs should be excluded, what distance from the indel edge is recommended? (I don't expect there to be an established distance but an approximation would be good.)

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