Number of callers in SURVIVOR merge tools for DEL

RajLabMSSM / AMP_AD_StructuralVariation

Repository for the AMP-AD structural variation manuscript

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Number of callers in SURVIVOR merge tools for DEL #3

Closed olivia-gc closed 1 week ago

olivia-gc commented 6 months ago

Hi, I just wanted some clarification on the 'merge tools' step for DEL in the pipeline. From my understanding DEL calls should overlap between be manta AND 2 callers? Or manta OR 2 callers?

I am trying to follow the pipeline, and from my understanding we call upon the SURVIVOR merge in the merge_and_benchmark_vcfs_truvari.sh script to merge the DEL tools. I am confused because in this script, there is SURVIVOR with min_num_calls=1. Any clarification would be very appreciated.

Thank you

ricardovialle commented 1 month ago

Hi, Sorry, I missed your question. The rule was all Manta calls plus any other deletion found by at least 2 other tools. Please let me know if you still need assistance.

Best, Ricardo