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CCRGeneticsBranch / khanlab_ngs_pipeline

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No cnvkit ouput for MTC001 case ids #24

Open vinegang opened 1 year ago

vinegang commented 1 year ago

Hsien-Chao noticed that MTC001 libraries did not generate output for cnvkit. On looking though the log/dryrun, it is evident that MTC001 libraries were processed using agilent.v7 kit and this is not added to the config file under sample captures for cnvkit.

     "cnvkit_ref"            :{
            "clin.ex.v1"            : "/data/Clinomics/Ref/khanlab/cnvkit/clin.ex.v1.hg19.cnn",
            "clin.snv.v1"           : "/data/Clinomics/Ref/khanlab/cnvkit/clin.snv.v1.hg19.cnn",
            "clin.cnv.v2"           : "/data/Clinomics/Ref/khanlab/cnvkit/clin.cnv.v2.hg19.cnn",
            "clin.snv.v2"           : "/data/Clinomics/Ref/khanlab/cnvkit/clin.snv.v2.hg19.cnn",
            "seqcapez.rms.v1"       : "/data/Clinomics/Ref/khanlab/cnvkit/seqcapez.rms.v1.hg19.cnn",
            "seqcapez.hu.ex.v3"     : "/data/Clinomics/Ref/khanlab/cnvkit/seqcapez.hu.ex.v3.hg19.cnn"

Solution:

Create a .cnn file for agilent.v7 kit and intergrate into the pipeline.