Checklist for adding the SN cohort for revision

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Snakemake pipeline steps

Alignment and quality control

• [x] align
• [x] fingerprint
• [x] gencode

Somatic variant calling

• [x] mutect
• [x] m2db

Copy number calling

• [x] cnv (gatk cnv)
• [x] titancna
• [x] sequenza

Expression

• [x] quant_tpm
• [x] tpm2db (manually run R function)
• [x] transcriptclass2db (manually run R function)

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Once the new cohorts are added, we need to create clean versions of the following tables for the revision (SNU only which has DNA + RNA)

Quality tables

• [x] analysis.gene_coverage
• [x] analysis.blocklist
• [x] analysis.coverage
• [x] analysis.rna_blocklist
• [x] analysis.gold_set
• [x] analysis.rna_silver_set
• [x] analysis.platinum_set

Clinical/metadata tables

• [x] analysis.tumor_pairs
• [x] analysis.rnaseq_pairs
• [x] analysis.analyte_sets
• [x] analysis.pairs
• [x] clinical.surgeries
• [x] analysis.files
• [x] clinical.cases
• [x] biospecimen_sample_types
• [x] biospecimen_samples
• [x] biospecimen.aliquots

Somatic variant tables

• [x] variants.ssm2_count
• [x] variants.anno
• [x] variants.passgeno
• [x] variants.pyclone_loci
• [x] variants.pyclone_cluster

Copy number tables

• [x] analysis.gatk_seg_stats
• [x] analysis.gatk_aneuploidy
• [x] variants.gatk_seg
• [x] variants.titan_seg
• [x] variants.seqz_seg
• [x] variants.titan_params
• [x] variants.seqz_params

Expression tables

• [x] analysis.transcriptional_subtypes
• [x] analysis.estimate_purity

Optional downstream tables that can be added later

• [ ] analysis.hypermutation
• [x] analysis.neoantigens_by_aliquot

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Closing as all required steps were completed in fall 2021.