Usage

This package provides a command line interface.

The Normalizer

To normalize a description variant:

$ mutalyzer_normalizer "NG_012337.1(NM_003002.2):c.274G>T"

Enable the file based cache

Create a cache directory and a configuration file:

$ mkdir cache
$ echo MUTALYZER_CACHE_DIR = $(pwd)/cache > config.txt

To ensure that any uncached references encountered during a Mutalyzer run will be added to the cache directory:

$ echo MUTALYZER_FILE_CACHE_ADD = true >> config.txt

Setup the email address used to communicate with the NCBI:

$ echo EMAIL = your.email@address.com >> config.txt

Optionally, setup the NCBI API key:

$ echo NCBI_API_KEY = your_NCBI_key >> config.txt

Populate the cache:

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_retriever --id NG_012337.3 --parse --split --output cache

For GRCh37 and GRCh38 chromosomal references (NC_):

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_retriever ncbi_assemblies --ref_id_start NC_ --assembly_id_start GRCh --output cache --include_sequence

Now the tool can be run with the cache:

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_normalizer "NC_000022.11(NM_182984.5):c.95del"

The Mapper

To map NM_003002.4:c.274G>T to the GRCh38 assembly chromosome:

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_mapper "NM_003002.4:c.274G>T" --reference-id GRCh38

To map NM_003002.2:c.274G>T to the GRCh38 assembly chromosome using the NM_003002.4 transcript:

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_mapper "NM_003002.4:c.274G>T" --reference-id GRCh38 --selector-id NM_003002.4

For the above note that the sequences are sliced to the transcript’s exons and that the variants introduced by the sequences differences are filtered out.

To map NG_012337.1(NM_003002.2):c.274G>T to NG_012337.3(NM_003002.4):

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_mapper "NG_012337.1(NM_003002.2):c.274G>T" --reference-id NG_012337.3 --selector-id NM_003002.4

To map NG_012337.1(NM_003002.2):c.274G>T to NG_012337.3(NM_003002.4) with variant filtering:

$ MUTALYZER_SETTINGS="$(pwd)/config.txt" mutalyzer_mapper "NG_012337.1(NM_003002.2):c.274G>T" --reference-id NG_012337.3 --selector-id NM_003002.4 --filter