tsoppy input standardization - 3. Fusions and splice variants

[danielvo]

Inputs considered so far:

• Dragen TSO500 analysis pipeline v. 2.6.2
  • the information below is based on output generated for samples sequenced with TSO500 assay version 2, but the current
  • unclear: is the Dragen server version a factor?
    • OUS assumes it does not, and both OUS and UNN use the same Dragen server version.
      • It looks like both assay v1 and assay v2 samples can now be analyzed with the same Dragen software.
    • Dragen server version [07.021.624.]3.11.2 was used when generating the output referenced in the text below
    • UNN utilizes the same Dragen server version and Dragen TSO500 analysis pipeline version
    • unclear: When analyzing samples with ICA (Illumina Cconnected Analysis), can one pick exactly the same Dragen server version and TSO500 pipeline version?
  • unclear: can the analysis output structure vary based on the sample sheet content/format choices?
    • different Pair_ID and Sample_ID values were used when generating the output referenced in the text below
    • we should aim to standardize the sample sheets across InPreD nodes either way
• Local App version 2.2.0.12
  • the sample sheet content/format (e.g., the Pair_ID value choice) can impact the analysis output structure
    • different Pair_ID and Sample_ID values were used when generating the output referenced in the text below

3. Fusions and splice variants

3.1 Input files

3.1.1. Fusion calling output

Dragen TSO500 2.6.2:

• file path: Logs_Intermediates/RnaFusion/<sample_ID>/<sample_ID>_AllFusion.csv

Local App 2.2.0.12:

• file path: Logs_Intermediates/RnaFusionMerge/<sample_ID>/<sample_ID>_AllFusions.csv

The Dragen output file seems to be backwards-compatible with the Local App output, but it contains four additional columns (the field descriptions shown below are taken directly from the Dragen output file header):

• Gene A Sense: Indicates whether left/right breakpoint order suggests fusion transcript is in the same sense of Gene A. If multiple genes in Gene A, then semicolon separated list of bools
• Gene A Location: Location of the breakpoint within Gene A: IntactExon: Matches exon boundary, BrokenExon: Inside an exon, Intronic: Within an intron, Intergenic: No gene overlap. If multiple genes in Gene A, then semi - colon separated list of values.
• Gene B Sense: Indicates whether left/right breakpoint order suggests fusion transcript is in the same sense of Gene B. If multiple genes in Gene B, then semi - colon separated list of bools
• Gene B Location: Location of the breakpoint within Gene B: IntactExon: Matches exon boundary, BrokenExon: Inside an exon, Intronic: Within an intron, Intergenic: No gene overlap If multiple genes in Gene B, then semi - colon separated list of values.

3.1.1. Splice variant calling output

Dragen TSO500 2.6.2:

• file path: Logs_Intermediates/RnaSpliceVariantCalling/<sample_ID>/<sample_ID>.tsv

Local App 2.2.0.12:

• file path: Logs_Intermediates/RnaSpliceVariantCalling/<sample_ID>/<sample_ID>.tsv

The file paths/names and the file formats seem to be identical for both pipelines, though the variant calls, their quality scores etc. (for a given sample/FASTQ input) do differ. While there may be no differences for the purposes of parsing, joint interpreting or mixing of results from the two pipelines should be done with caution.

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It seems that one could re-use much of the post-processing/re-formatting utilized by TSOPPI, but InPreD personnel that works with fusions and splice variants should probably discuss what changes should be made (AHUS has shared some scripts for making TSOPPI output more suitable for FuSViz use - one could probably implement the necessary changes in tsoppy directly).