Path’s to know

On JUNO

General

/opt/common

Where one can find the programs such as bwa, igv, R etc.

• Sub-directories include: CentOS_7/<program>/<version> and CentOS_7-dev/<program>/<version>.
• If you created or found a new tool that should be installed globally for everyone to use, then contact at HPC to get it installed under /opt/common/CentOS_7-dev.

/ifs/dmpshare

Space where clinical data from DMP is stored

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CMO ACCESS

/work/access/production/runs/

This is where all the requests are currently being stored for data generated on MSK-ACCESS run in CMO.

/work/access/production/runs/NYS_validation/current

This is where all the DMP runs that were used for New York State validation are currently being stored for MSK-ACCESS.

/work/access/production/resources/

Here we have following resources:

• admie - Files used for micro-satellite instability detection tool ADMIE for MSK-ACCESS
• cosmic - VCF file of cosmic used in MSK-ACCESS workflows
• dbSNP - VCF file of dbSNP used in MSK-ACCESS workflows
• exac - VCF file of ExAC used in MSK-ACCESS workflows
• mills-and-1000g - VCF file of mills-and-1000g used in MSK-ACCESS
• reference - reference genome file used in MSK-ACCESS workflows
• tools - general packages used in MSK-ACCESS workflows
• msk-access - Data specific resources for MSK-ACCESS workflows. This include the following:
  • hiseq4000_curated_duplex_bams_dmp - curated DMP duplex BAMS from HiSeq 4000
  • novaseq_curated_simplex_bams_dmp - curated DMP simplex BAM from NovaSeq.
  • hiseq4000_curated_simplex_bams_dmp - curated DMP simplex BAM from HiSeq 4000
  • novaseq_curated_standard_bams_dmp - curated DMP standard BAM from NovaSeq
  • hiseq4000_curated_standard_bams_dmp - curated DMP standard BAM from HiSeq 4000
  • novaseq_curated_unfiltered_bams_dmp - curated DMP unfiltered BAM from NovaSeq
  • hiseq4000_curated_unfiltered_bams_dmp - curated DMP unfiltered BAM from HiSeq 4000
  • novaseq_unmatched_normal_plasma_duplex_bams_dmp - DMP unmatched normal plasma duplex BAM from NovaSeq
  • hiseq4000_unmatched_normal_plasma_duplex_bams_dmp - DMP unmatched normal plasma duplex BAM from HiSeq 4000
  • novaseq_unmatched_normal_plasma_standard_bams_dmp - DMP unmatched normal plasma standard BAM from NovaSeq
  • hiseq4000_unmatched_normal_plasma_standard_bams_dmp - DMP unmatched normal plasma standard BAM from HiSeq 4000
  • novaseq_curated_duplex_bams_dmp - curated DMP duplex BAMS from NovaSeq
  • regions_of_interest - Different interval files describing regions of interest for MSK-ACCESS assay
• If we can justify adding data/tools to the above mentioned location please contact Ronak Shah.

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