ACCESS Operators

Operators related to ACCESS workflows

On the ACCESS team we leverage these operators for our cfDNA workflows:

AccessLegacyOperator (BAM and Quality Control Workflow)

This operator is triggered from a call to /v0/operator/run/request by a given IGO request ID with pipeline name access legacy

• Objects used:

  • File

    • fastq

  • FileMetadata fields:

    • cmoSampleClass

    • sampleName

    • patientId

• Important logic:

  • A txt "title file" is generated as part of the inputs file

  • Samples are grouped and submitted in batches of 20

  • Suffixes are added to the patientId field to prevent samples from being paired through Abra

  • A dummy SampleSheet.csv file is used as an input to the Marianas tool

AccessLegacySNVOperator (SNV and INDELs workflow)

This operator is triggered from a call to /v0/operator/run/request by a given IGO request ID with pipeline name access legacy snv

• Objects used:

  • File

    • duplex tumor bam (IGO)

    • unfiltered normal bam (either IGO or DMP)

    • matched duplex tumor bams IGO / DMP (for genotyping only)

    • matched simplex tumor bams IGO / DMP (for genotyping only)

    • ACCESS curated bams (grouped by the access_curated_normals file group)

  • FileMetadata fields:

    • cmoSampleClass

    • sampleName

    • patientId (used for pairing Tumor with Normal)

• Important logic:

  • Tumor bams from the given request ID are paired with the most recent normal associated with the given patient ID (for genotyping step)

  • Tumor bams are paired with the following hi-depth, duplex buffy coat normal:

    • DONOR22-TP_cl_aln_srt_MD_IR_FX_BR__aln_srt_IR_FX-duplex.bam

  • Genotyping bams are queried from the access_curated_normals file group and used as control samples

AccessLegacySVOperator (Structural Variants workflow)

This operator is triggered from a call to /v0/operator/run/request by a given IGO request ID with pipeline name access legacy sv

• Objects Used:

  • File

    • tumor standard bams (from access legacy pipeline outputs)

    • ACCESS default SV normal (high-depth standard bam)

  • FileMetadata fields:

    • sampleName

• Important logic:

  • Tumors and paired with the following hi-depth, standard buffy-coat normal:

    • DONOR22-TP_cl_aln_srt_MD_IR_FX_BR.bam

AccessLegacyMSIOperator (Microsatellite Instability workflow)

• Objects Used:

  • File:

    • T/N standard bams (from access legacy pipeline outputs)

  • FileMetadata fields:

    • sampleName

• Important logic:

  • Tumors are paired with most recent normal with the same patient ID

AccessLegacyCNVOperator (Copy Number Variants workflow)

• Objects Used:

  • File:

    • Tumor unfiltered bams (from access legacy pipeline outputs)

  • FileMetadata fields:

    • sampleName

• Important logic:

  • Tumors are paired with a panel of unfiltered normals found in the normals text file