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Analysis steps for RCC paired tumor (plasma) - normal (buffy coat) amplicon datasets:

  1. Download datasets from Galaxy histories on main:

    $ python ~/gwu/galaxy/download_history_datasets.py

  2. Run analyses for a plate of data. This create many files; we care most about the BAM for each sample.

    $ make run_dir TARGET_DIR=~/projects/rcc/Plate8
// Move results to Plate8 directory
$ make run_dir TARGET_DIR=~/projects/rcc/Plate9
// Move results to Plate9 directory

  3. Run matched tumor-normal analysis for plasma-buffy coat for each sample

    // Move Plate8 results back to main directory
$ make run_paired_somatic

    NOTES: needed to fix freebayes-parallel script to point to correct location for vcffirstheader and vcfstreamsort in conda. vcfstreamsort is in vcflib directory, but vcffirstheader needs to be added: https://github.com/vcflib/vcflib/blob/8ac9fd517579134ef3b9797714d20c9c99c18ec6/bin/vcffirstheader

  4. Do final query

    $ make query_all

  5. NOTE: for FFPE samples matched to a plasma/buffy coat sample (e.g. plate7), steps 3 and 4 must be replaced with:

    $ make ffpe_samples
$ make ffpe_reports