Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GermlineCNVCaller Assertion Error: Some samples do not have read depth metadata

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    Hayden Shinn

    I am also having the exact same error. Were you ever able to figure it out? Xscrapert

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    Andrey Smirnov

    Hi Xscrapert,

    I apologize for the late response. It looks like in your DetermineContigPloidy command you set path to /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_cases_ploidy and as ploidy input GermlineCNVCaller takes /paedyl01/disk1/yangyxt/wesplus/healthy_bams_for_CNV/using_iGT359V1_probe/iGT359V1_case_ploidy - note the difference in the directory spelling.

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