Forum Login Issue:
Currently the "Log in with Google" button redirects you to a "Page not found." This is an issue that our forum vendors are working on fixing. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
ex: https://gatkforums.broadinstitute.org/gatk/gatk/entry/...

WDL script is not copying the index files for the reference genome from its directory

NandaNanda CanadaMember
  • The input json file has three inputs (reference, intervalBED, and BAMlist).
  • reference : Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa
  • intervalBED: Sequencing_kits/Roche/SeqCap/interval_list.bed
  • BAMlist: Sequencing_data/ProjectA/BAM_files.list

  • In human reference directory, I have the following files: genome.fa and genome.fa.fai, genome.dict

  • WDL script is successfully copying the reference file from its directory and making a copy of it while creating a session for each run. But it fails to copy the "FASTA index file".

Is there any way, I can refer the index file in GATK command?

Tagged:

Answers

Sign In or Register to comment.