Test-drive the GATK tools and Best Practices pipelines on Terra
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Usage of "--dontUseSoftClippedBases" HaplotypeCaller option for exom enrichment data
Hi GATK Team,
HaplotypeCaller does not call structural variants from soft clipped bases, therefore the "--dontUseSoftClippedBases" should mainly reduce false positives (e.g. incomplete adapter trimming)? Is this thought correct or am i wrong?
Greetings from Munich