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seq-validation

Workflows for validating sequence data

validate-bam :

This WDL performs format validation on SAM/BAM files in a list

Requirements/expectations :

  • One or more SAM or BAM files to validate
  • Explicit request of either SUMMARY or VERBOSE mode in inputs.json

Outputs:

  • Set of .txt files containing the validation reports, one per input file

Cromwell version support

  • Successfully tested on v49
  • Does not work on versions < v23 due to output syntax

Important Notes :

Contact Us :

  • The following material is provided by the Data Science Platforum group at the Broad Institute. Please direct any questions or concerns to one of our forum sites : GATK or Terra.

LICENSING :

Copyright Broad Institute, 2019 | BSD-3 This script is released under the WDL open source code license (BSD-3) (full license text at https://github.com/openwdl/wdl/blob/master/LICENSE). Note however that the programs it calls may be subject to different licenses. Users are responsible for checking that they are authorized to run all programs before running this script.