Add mix and match functionality for mutation calling (resolves #265)#283
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Add mix and match functionality for mutation calling (resolves #265)#283
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arkal
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Looking good. Minor edits needed. Also, Make sure you add an entry in MANUAL.md.
| job.fileStore.logToMaster('Aggregated mutations for %s successfully' % univ_options['patient']) | ||
| return merged_snvs.rv() | ||
| chroms = {} | ||
| for caller in mutation_results: |
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Document why you've done this
| @@ -105,25 +121,27 @@ def merge_perchrom_mutations(job, chrom, mutations, univ_options): | |||
| # For now, let's just say 2 out of n need to call it. | |||
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remove these redundant comments
| if 'strelka' + mut_type in perchrom_mutations: | ||
| perchrom_mutations['strelka'] = perchrom_mutations['strelka_' + mut_type] | ||
| perchrom_mutations.pop('strelka_' + mut_type) | ||
| if not perchrom_mutations: |
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This condition should occur before # process the strelka key
| perchrom_mutations.pop('strelka_' + mut_type) | ||
| if not perchrom_mutations: | ||
| continue | ||
| majority = 1 if len(perchrom_mutations) <= 2 else len(perchrom_mutations) / 2 |
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(len(perchrom_mutations) + 1) / 2
src/protect/pipeline/ProTECT.py
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| # Flags to check for presence of encryption keys if required | ||
| gdc_inputs = ssec_encrypted = False | ||
| gdc_inputs = ssec_encrypted = sample_without_variants = False |
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# Flags to check for presence of encryption keys if required
gdc_inputs = ssec_encrypted = False
# Flag to check if a sample without an input vcf/bedpe was provided
sample_without_variants = False
src/protect/pipeline/ProTECT.py
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| raise ParameterError('Cannot run ProTECT using GDC RNA bams. Please fix ' | ||
| 'sample %s' % sample_name) | ||
| gdc_inputs = True | ||
| if 'mutation_vcf' not in sample_set[sample_name] and 'fusion_bedpe' not in sample_set[sample_name]: |
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arkal
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arkal
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May 18, 2018
| # Process the strelka key | ||
| perchrom_mutations['strelka'] = perchrom_mutations['strelka_' + mut_type] | ||
| perchrom_mutations.pop('strelka_' + mut_type) | ||
| if 'strelka' + mut_type in perchrom_mutations: |
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This should be if 'strelka_' + mut_type in perchrom_mutations:
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MANUAL.md
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| mutation_calling: | ||
| consensus: | ||
| indel_majority: None -> Number of callers required to accept an indel. |
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remove the 'None'. Say default is to compute it dynamically. Same for snv
src/protect/pipeline/defaults.yaml
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| mutation_calling: | ||
| consensus: | ||
| indel_majority: None |
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make this
consensus:
indel_majority:
snv_majority:
| # version: 1.2.0 | ||
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| mutation_calling: | ||
| consensus: |
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Make this
consensus:
# indel_majority: 1 # The number of callers required to accept an indel
# snv_majority: 2 # The number of callers required to accept an snv
arkal
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May 19, 2018
src/protect/pipeline/ProTECT.py
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| else: | ||
| count = 1 if tool_options['strelka']['run'] is True else 0 | ||
| if tool_options['consensus'][mut_type + '_majority'] > count: | ||
| raise RuntimeError('Majority cannot be greater than the number of callers. Got number of %s callers ' |
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added 2 commits
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resolves #265
Added functionality so the user can select which mutation callers to execute. If no mutation callers are selected, the user must provide at least a mutation_vcf or a fusion_bedpe file.