output (split between two output folders):
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output/
Consensus (best) tree output:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/consensus_tree
Checklist
[x] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
[x] This PR does NOT contain molecular files, compressed files, output files such as images (e.g..png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
[x] I have set up or verified the main branch protection rule following the github standards before opening this pull request.
[x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
[x] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
Description
Launch SomatiSniper + Battenberg + PhyloWGS + seeds [HSNC single-region] Seed + Sample combination that does not work due to mcmc number https://github.com/uclahs-cds/project-method-AlgorithmEvaluation-BNCH-000082-SRCRNDSeed/issues/63
Changed
/hot/users/psteinberg/git/project-SRC-RandomSeed/src/output-analysis/parsing/run_parse_consensus_tree_PhyloWGS.sh
to parse SomaticSniper-Battenberg-PhyloWGS output.Closes #63
Pipeline Run Results
sample:
ILHNLNEV000001-T001-P01-F
seed:51404
input SNV (SomaticSniper):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/SNV/somaticsniper/recsnv/vcfs/ILHNLNEV000001-T001-P01-F.vcf
input CNA (Battenberg):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/ILHNLNEV000001-T001-P01-F/ILHNLNEV000001-T001-P01-F_cellularity_ploidy.txt
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/ILHNLNEV000001-T001-P01-F/ILHNLNEV000001-T001-P01-F_subclones.txt
config:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/input/config/seed_51404.config
yaml:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/somaticsniper_battenberg_yamls/single-region/ILHNLNEV000001-T001-P01-F.yaml
output (split between two output folders):
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output/
PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg-mutass.json.gz
PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg-muts.json.gz
PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg-summ.json.gz
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/call-SRC-1.1.0/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output
PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg.mutass.json.gz
PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg.muts.json.gz
PhyloWGS-2205be1_{seed}_ILHNLNEV000001-T001-P01-F_StomaticSniper-Battenberg.summ.json.gz
logs:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/logs/
witness data:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/witness_results/
Consensus (best) tree output:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-somaticsniper-battenberg-phylowgs/output/consensus_tree
Checklist
.png
, .jpeg
),.pdf
,.RData
,.xlsx
,.doc
,.ppt
, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.main
branch protection rule following the github standards before opening this pull request.CHANGELOG.md
under the next release version or unreleased, and updated the date.