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Sometimes the signature of a long indel in a bam (before reassembly, that is) is long soft clips at the end of reads. If these soft clips are long and high quality we need to recognize them as compelling evidence of variation in Mutect's active region determination. Currently all soft clips are weighted about as heavily as SNVs, which is too little in the case of long soft clips.
The text was updated successfully, but these errors were encountered:
Sometimes the signature of a long indel in a bam (before reassembly, that is) is long soft clips at the end of reads. If these soft clips are long and high quality we need to recognize them as compelling evidence of variation in Mutect's active region determination. Currently all soft clips are weighted about as heavily as SNVs, which is too little in the case of long soft clips.
The text was updated successfully, but these errors were encountered: