| fusion_id | direct_support | discordant_support | total_support | effect | topo | chr3 | exon3 | gene3 | transcript3 | bp3 | chr5 | exon5 | gene5 | transcript5 | bp5 | new_whitelist | new_reportable | self_fusion | is_hard_filtered | meets_support_criteria | contains_relevant_domains_3 | contains_relevant_domains_5 | fusion_domains | order_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| be1f8268-44ee-4c99-b0db-e4766db2c977 | 30 | 28 | 58 | in-frame | NaN | 10 | 18.0 | FGFR2 | ENST00000457416 | 123242706 | 5 | 2.0 | SUB1 | ENST00000265073 | 32589733 | False | False | False | False | False | False | False | [] | 22fwudfy | |
| 24a800ce-1d7b-4ce8-9c9a-041508bbbc99 | 30 | 28 | 58 | in-frame | NaN | 5 | 3.0 | SUB1 | ENST00000265073 | 32589733 | 10 | 17.0 | FGFR2 | ENST00000457416 | 123242706 | False | False | False | False | False | False | True | [] | 22fwudfy |
| class: Workflow | |
| cwlVersion: v1.0 | |
| id: access_qc_aggregator | |
| label: access_qc_aggregator | |
| $namespaces: | |
| sbg: 'https://www.sevenbridges.com/' | |
| inputs: | |
| - id: duplex_extraction_files | |
| type: | |
| type: array |
| access_filems = FileMetadata.objects.filter(metadata__recipe='MSK-ACCESS_v1', file__file_type__name='fastq') | |
| access_request_ids = set([f.metadata['requestId'] for f in access_filems]) | |
| # --> 103 ACCESS request IDs total | |
| duplicates = File.objects\ | |
| .filter( | |
| filemetadata__metadata__requestId__in=access_request_ids, | |
| file_type__name='fastq' |
| /work/access/production/runs/voyager/staging/small_variants/50948a4f-c4b8-4856-97e5-ece000ddc3d4 | |
| /work/access/production/runs/voyager/staging/small_variants/7511548f-f695-497e-9558-51b3d63d27ac | |
| /work/access/production/runs/voyager/staging/small_variants/a99cf55e-ad09-44f6-b50e-44cf4169960b | |
| /work/access/production/runs/voyager/staging/small_variants/fcee2eec-7a7f-4eba-9bfa-841e5234f49f | |
| /work/access/production/runs/voyager/staging/small_variants/7cc7c0c1-b1d5-477a-909e-897362ba3cb5 | |
| /work/access/production/runs/voyager/staging/small_variants/547fc37c-fd79-4de1-9013-86f69fb89c27 | |
| /work/access/production/runs/voyager/staging/small_variants/85189928-d546-4be0-8542-983d556c16a1 | |
| /work/access/production/runs/voyager/staging/small_variants/430b9606-2583-441e-8a2d-f216a4ed97e5 | |
| /work/access/production/runs/voyager/staging/small_variants/eabeb028-0d6e-48e8-aff5-33d1f0be99ce | |
| /work/access/production/runs/voyager/staging/small_variants/f44cfe07-e633-4c48-92dd-2a22ccc6a83e |
| import json | |
| import requests | |
| paths = [ | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/curated_normal_manifest.txt", | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/ACCESS_targets_coverage.bed", | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/ACCESS_targets_coverage.txt", | |
| "/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/microsatellites.list", | |
| "/juno/work/access/production/resources/admie/versions/v1.0/ADMIE.joblib" | |
| ] |
| import requests | |
| gene_list = { | |
| 'path': '/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/juber-hg19-gene-list.bed', | |
| 'file_type': 'bed', | |
| } | |
| hotspots = { | |
| 'path': '/juno/work/access/production/resources/msk-access/v1.0/regions_of_interest/versions/v1.0/hotspot-list-union-v1-v2_with_TERT.txt', | |
| 'file_type': 'txt', |
| # Params | |
| mutect_params: | |
| dcov: 5000 | |
| read_filter: ['BadCigar'] | |
| fraction_contamination: 0.0005 | |
| minimum_mutation_cell_fraction: 0.0005 | |
| vardict_params: | |
| allele_freq_thres: 0.0005 | |
| min_num_variant_reads: 1 |
| singularity run -B /folder/with/tumor_normal/bams:/tmp /home/johnsoni/brass/quay_io-brass_v6.3.0.simg | |
| brass.pl -c 2 -o myout -t /tmp/tumor.bam -n /tmp/normal.bam | |
| # causes error - why is -d required? ask Peter... |
| # Uses bsub with rsync to copy large folders | |
| # | |
| # Uses a walltime limit of 60 hours (should be enough for very large folders) | |
| # | |
| # Runs in parallel across each subfolder of the source folder, and creates logs for each as well | |
| # | |
| # Usage: python bsub_copy.py /source/folder /dest/folder | |
| import os | |
| import sys |