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Input files to GatherBqsrReports

awengerawenger Stanford UniversityMember

The usage for the GatherBqsrReports tool implies that it accepts a list of files as input (i.e. a .list file). In practice, it accepts raw .table files.

// Does not work

echo "in.table" > files.list
java -cp GATK.jar org.broadinstitute.gatk.tools.GatherBqsrReports I=files.list O=out.table
// Bad input: The GATK report has an unknown/unsupported version in the header: in.table

// Does work

java -cp GATK.jar org.broadinstitute.gatk.tools.GatherBqsrReports I=in.table O=out.table
java -cp GATK.jar org.broadinstitute.gatk.tools.GatherBqsrReports I=in1.table I=in2.table O=out.table

// Usage
// I=File List of scattered BQSR files
// O=File File to output the gathered file to

Could you update GatherBqsrReports to accept a .list? I always prefer to pass in a .list instead of multiple options on the command line to avoid exceeded the command line buffer.

Issue · Github
by Sheila

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  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    This is a new tool so we need to check the intended behavior. Unfortunately this is a different type of tool compared to most other GATK tools, which doesn't inherit the list-processing abilities conferred by the engine. We may have forgotten to build that capability into this tool. If so we'll put this on the todo list since it's obviously a desirable feature. We'll keep you informed once we get some answers from the tool's original author.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @awenger, this functionality has just been added and merged into the development version. It will be available starting in the next nightly build.

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