===== Usage ===== Currently this module only supports genotyping and merging small variants (SNV and INDELS). For this we have the following command line submodule called **small_variants**. Which have the following sub-commands: * `generate`_: To run GetBaseCountMultiSample on given BAM files * `merge`_: To merge MAF format files w.r.t counts generated from the `generate` command. * `all`_: This will run both of the sub-commands above `generate` and `merge` togather. * `multiple-samples`_: This will run sub-commands `all` for multiple patients in the provided metadata file generate -------- To use `small_variants generate` via command line here are the options:: > genotype_variants small_variants generate --help Usage: genotype_variants small_variants generate [OPTIONS] Command that helps to generate genotyped MAF, the output file will be labeled with the patient identifier as prefix, or sample identifier. Sample identifier is prioritized over patient identifier. Options: -i, --input-maf PATH Full path to small variants input file in MAF format [required] -r, --reference-fasta PATH Full path to reference file in FASTA format [required] -p, --patient-id TEXT Alphanumeric string indicating patient identifier [required] -si, --sample-id TEXT Alphanumeric string indicating sample identifier -b, --standard-bam PATH Full path to standard bam file, Note: This option assumes that the .bai file is present at same location as the bam file -d, --duplex-bam PATH Full path to duplex bam file, Note: This option assumes that the .bai file is present at same location as the bam file -s, --simplex-bam PATH Full path to simplex bam file, Note: This option assumes that the .bai file is present at same location as the bam file -g, --gbcms-path PATH Full path to GetBaseCountMultiSample executable with fragment support [required] -fd, --filter-duplicate INTEGER Filter duplicate parameter for GetBaseCountMultiSample -fc, --fragment-count INTEGER Fragment Count parameter for GetBaseCountMultiSample -mapq, --mapping-quality INTEGER Mapping quality for GetBaseCountMultiSample -t, --threads INTEGER Number of threads to use for GetBaseCountMultiSample -v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or DEBUG --help Show this message and exit. .. code-block:: console genotype_variants small_variants generate \ -i /path/to/input_maf \ -r /path/to/reference_fasta \ -g /path/to/GetBaseCountsMultiSample \ -p patient_id \ -b standard_bam \ -d duplex_bam \ -s simplex_bam Expected Output """"""""""""""" In the current worrking directory if the above command is executed you will find the following files: * patient_id-STANDARD_genotyped.maf * patient_id-DUPLEX_genotyped.maf * patient_id-SIMPLEX_genotyped.maf merge ----- To use `small_variants merge` via command line here are the options:: > genotype_variants small_variants merge --help Usage: genotype_variants small_variants merge [OPTIONS] Given original input MAF used as an input for GBCMS along with GBCMS generated output MAF for standard_bam, duplex_bam or simplex bam, Merge them into a single output MAF format. If both duplex_bam and simplex_bam based MAF are provided the program will generate merged genotypes as well. The output file will be based on the give alphanumeric patient identifier as suffix. Options: -i, --input-maf PATH Full path to small variants input file in MAF format used for input to GBCMS for generating genotypes -std, --input-standard-maf PATH Full path to small variants input file in MAF format generated by GBCMS for standard_bam -d, --input-duplex-maf PATH Full path to small variants input file in MAF format generated by GBCMS for duplex_bam -s, --input-simplex-maf PATH Full path to small variants input file in MAF format generated by GBCMS for simplex_bam -p, --patient-id TEXT Alphanumeric string indicating patient identifier [required] -si, --sample-id TEXT Alphanumeric string indicating sample identifier -v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or DEBUG --help Show this message and exit. .. code-block:: console genotype_variants small_variants merge \ -i /path/to/input_maf \ -std /path/to/standard_bam_genotyped_maf \ -d /path/to/duplex_bam_genotyped_maf \ -s /path/to/simplex_bam_genotyped_maf \ -p patient_id \ Expected Output """"""""""""""" In the current worrking directory if the above command is executed you will find the following files: * patient_id-ORG-STD-SIMPLEX-DUPLEX_genotyped.maf If only input_maf with duplex_bam_genotyped_maf and simplex_bam_genotyped_maf is given then the output file will be: * patient_id-ORG-SIMPLEX-DUPLEX_genotyped.maf If only standard_bam_genotyped_maf with duplex_bam_genotyped_maf and simplex_bam_genotyped_maf is given then the output file will be: * patient_id-STD-SIMPLEX-DUPLEX_genotyped.maf If only duplex_bam_genotyped_maf and simplex_bam_genotyped_maf is given then the output file will be: * patient_id-SIMPLEX-DUPLEX_genotyped.maf all --- To use `small_variants all` via command line here are the options:: > genotype_variants small_variants all --help Usage: genotype_variants small_variants all [OPTIONS] Command that helps to generate genotyped MAF and merge the genotyped MAF. The output file will be based on the give alphanumeric patient identifier as prefix, or sample identifier. Sample identifier is prioritized over patient identifier. Options: -i, --input-maf PATH Full path to small variants input file in MAF format [required] -r, --reference-fasta PATH Full path to reference file in FASTA format [required] -p, --patient-id TEXT Alphanumeric string indicating patient identifier [required] -si, --sample-id TEXT Alphanumeric string indicating sample identifier -b, --standard-bam PATH Full path to standard bam file, Note: This option assumes that the .bai file is present at same location as the bam file -d, --duplex-bam PATH Full path to duplex bam file, Note: This option assumes that the .bai file is present at same location as the bam file -s, --simplex-bam PATH Full path to simplex bam file, Note: This option assumes that the .bai file is present at same location as the bam file -g, --gbcms-path PATH Full path to GetBaseCountMultiSample executable with fragment support [required] -fd, --filter-duplicate INTEGER Filter duplicate parameter for GetBaseCountMultiSample -fc, --fragment-count INTEGER Fragment Count parameter for GetBaseCountMultiSample -mapq, --mapping-quality INTEGER Mapping quality for GetBaseCountMultiSample -t, --threads INTEGER Number of threads to use for GetBaseCountMultiSample -v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or DEBUG --help Show this message and exit. .. code-block:: console genotype_variants small_variants all \ -i /path/to/input_maf \ -r /path/to/reference_fasta \ -g /path/to/GetBaseCountsMultiSample \ -p patient_id \ -b standard_bam \ -d duplex_bam \ -s simplex_bam Expected Output """"""""""""""" Please refer to the `generate` and `merge` usage for the expected output. multiple-samples ---------------- To use `small_variants multiple-samples` via command line here are the options:: genotype_variants small_variants multiple-samples --help Usage: genotype_variants small_variants multiple-samples [OPTIONS] Command that helps to generate genotyped MAF and merge the genotyped MAF for multiple patients. the output file will be labelled with sample identifier as prefix Expected header of metadata_file in any order: sample_id maf standard_bam duplex_bam simplex_bam For maf, standard_bam, duplex_bam and simplex_bam please include full path to the file. Options: -i, --input-metadata PATH Full path to metadata file in TSV/EXCEL format, with following headers: sample_id, maf, standard_bam, duplex_bam, simplex_bam. Make sure to use full paths inside the metadata file [required] -r, --reference-fasta PATH Full path to reference file in FASTA format [required] -g, --gbcms-path PATH Full path to GetBaseCountMultiSample executable with fragment support [required] -fd, --filter-duplicate INTEGER Filter duplicate parameter for GetBaseCountMultiSample -fc, --fragment-count INTEGER Fragment Count parameter for GetBaseCountMultiSample -mapq, --mapping-quality INTEGER Mapping quality for GetBaseCountMultiSample -t, --threads INTEGER Number of threads to use for GetBaseCountMultiSample -v, --verbosity LVL Either CRITICAL, ERROR, WARNING, INFO or DEBUG --help Show this message and exit. .. code-block:: console genotype_variants small_variants multiple-samples \ -i /path/to/input_metadata \ -r /path/to/reference_fasta \ -g /path/to/GetBaseCountsMultiSample Expected Output """"""""""""""" Please refer to the `generate` and `merge` usage for the expected output. To use genotype_variants in a project:: import genotype_variants