Variant search

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Requirements

Variant search requires https://github.com/Mykrobe-tools/mykrobe to be installed and BIGSI >= v0.3.5

You can use BIGSI to search for DNA or Amino acid variants.

e.g. to search for samples with a G->T mutation at position 100 in the Mycobacterium Tuberculosis reference the command would be:

DNA variant search

bigsi variant_search --config config.yaml NC_000962.3.fasta G 100 T

To search for the rifampicin resistance mutation rpob_S450L the command would be as follows. Genbank files are required for these queries in order to map AA coordianates to DNA coordinates, and BIGSI is queried using the resulting DNA alleles.

Amino Acid variant search

bigsi variant_search --config config.yaml --genbank NC_000962.3.gb --gene rpoB NC_000962.3.fasta S 450 L