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hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Apache License 2.0
83 stars 21 forks source link

Make indel realignment splice aware #615

Open hammer opened 7 years ago

ihodes commented 7 years ago

The GATK indel realigner errors on reads with N in the CIGAR string, or will drop them with a CLI option. At the very least, we should be able to ignore them and keep those reads in the output BAM file.