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.

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.

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.

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.

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

Usage¶

generate¶

Expected Output¶

merge¶

Expected Output¶

all¶

Expected Output¶

multiple-samples¶

Expected Output¶

genotype_variants

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