Add fusion filters for transgene (resolves #237)

Added all fusion parameters to the input config so users can control
what fusion filters are applied.

MANUAL.md

@@ -414,6 +414,11 @@ be substituted with S3 links. Descriptions for creating all files can be found i
   gencode_transcript_fasta : /path/to/gencode_transcripts.faa -> The transcript file for the gencode gtf.
   gencode_annotation_gtf : /path/to/gencode_annotation.gtf -> The gencode genome annotation file.
   genome_fasta : /path/to/hg19.faa -> The gencode genome fasta file
+  filter_mt_fusions: True -> Switch to filter mitochondrial gene pairs
+  filter_ig_pairs: True -> Switch to filter immunoglobulin gene pairs
+  filter_rna_gene_fusions: True -> Switch to filter rna-gene pairs
+  filter_readthroughs: True -> Switch to filter readthroughs
+  readthrough_threshold: 500000 -> Threshold below which pairs will be called readthroughs
   version: 2.2.2
 
  haplotyping:

src/protect/mutation_translation.py

@@ -90,7 +90,8 @@ def run_transgene(job, snpeffed_file, rna_bam, univ_options, transgene_options,
  '--pep_lens', '9,10,15',
  '--cores', str(transgene_options['n']),
  '--genome', input_files['genome.fa'],
- '--annotation', input_files['annotation.gtf']]
+ '--annotation', input_files['annotation.gtf'],
+ '--log_file', '/data/transgene.log']
 
  if snpeffed_file is not None:
  parameters.extend(['--snpeff', input_files['snpeffed_muts.vcf']])
@@ -110,6 +111,15 @@ def run_transgene(job, snpeffed_file, rna_bam, univ_options, transgene_options,
  fusion_files = {key: docker_path(path) for key, path in fusion_files.items()}
  parameters += ['--transcripts', fusion_files['transcripts.fa'],
  '--fusions', fusion_files['fusion_calls']]
+ if transgene_options['filter_mt_fusions'] is True:
+ parameters.append('--filter_mt')
+ if transgene_options['filter_ig_pairs'] is True:
+ parameters.append('--filter_ig')
+ if transgene_options['filter_rg'] is True:
+ parameters.append('--filter_rna_gene_fusions')
+ if transgene_options['filter_readthroughs'] is True:
+ parameters.append('--filter_rt')
+ parameters.extend(['--rt_threshold', transgene_options['readthrough_threshold']])
 
  docker_call(tool='transgene',
  tool_parameters=parameters,

src/protect/pipeline/defaults.yaml

@@ -88,6 +88,11 @@ mutation_annotation:
 
 mutation_translation:
  transgene:
+ filter_mt_fusions: True
+ filter_ig_pairs: True
+ filter_rna_gene_fusions: True
+ filter_readthroughs: True
+ readthrough_threshold: 500000
  version: 2.5.0
 
 haplotyping:

src/protect/pipeline/input_parameters.yaml

@@ -133,6 +133,11 @@ mutation_translation:
  gencode_peptide_fasta : S3://protect-data/hg38_references/gencode.v25.pc_translations_NOPARY.fa.tar.gz
  gencode_transcript_fasta : S3://protect-data/hg38_references/gencode.v25.pc_transcripts_NOPARY.fa.tar.gz
  gencode_annotation_gtf : S3://protect-data/hg38_references/gencode.v25.annotation_NOPARY.gtf.tar.gz
+ filter_mt_fusions: True
+ filter_ig_pairs: True
+ filter_rna_gene_fusions: True
+ filter_readthroughs: True
+ readthrough_threshold: 500000
  genome_fasta : S3://protect-data/hg38_references/hg38.fa.tar.gz
  # version: 2.2.2