CleanVcf improvements #913
Description
- Resolve minor differences in run on featured workspace data.
- Subset or shard to enable running on larger cohorts.
- Write integration tests - use ArgumentsBuilder and/or runCommandLineProgram.
- Migrate SVReviseOverlappingMultiallelics into a simpler task that uses bedtools or bcftools.
- Integrate overlap functionality into existing GATK infrastucture.