GATK GermlineCNVCaller

Question

[giacuong171]

Hi guys, does anyone here have experience with GATK GermlineCNVCaller. I'm testing it right now with 3 samples in cohort mode. However, it took me so long, and seems never to end. Does anyone encounter the same problem?

a=""
    for i in {input.tsv}; do a=$a" -I "$i; done
    docker run -v {params.mount_dir}:{params.mount_dir} --cpus={threads} broadinstitute/gatk:latest /bin/bash -c \\
    "gatk --java-options "{params.mem}" GermlineCNVCaller \\
        --run-mode COHORT \\
        --annotated-intervals {input.anno} \\
        --interval-merging-rule OVERLAPPING_ONLY \\
        -L {input.interval} \\
        $a \\
        --contig-ploidy-calls {input.ploidy_calls} \\
        --output {params.dir} \\
        --output-prefix {params.prefix} \\
        --verbosity DEBUG"