REVertant MUTation find & verify (REVMUT)

REVMUT can help to find and verify putative revertant mutations (PRMs) in DNA sequence data. Common workflow is:

1. Find PRMs (deletions of given mutation, indels that restore the reading frame)
2. Annotatote PRMs with Oncotator to get transcript change of putative revertant mutations in HGVS format
3. Verify if one of the transcript change in HGVS format is revertant by looking how the length of the protein changes

There are scripts to do 1 and 3. Steps 2 might be added at a later stage in development.

Installation

pip install revmut

Find

The finding module takes a mutation and finds PRMs that:

• Delete the entire given mutation

• Restore the reading frame in case the given mutation (GM) is an indel. The criterium is:

  length(PRM) +/- length(GM) % 3 == 0
  

Run with:

revmut-find tests/test_data/human_g1k_v37_chr17.fa \
            tests/test_data/germline_mutations/T1_test_mutation.tsv \
            tests/test_data/T1.bam \
            tests/test_data/N1.bam > tests/test_data/output/T1_test.tsv

View input/output files:

• tests/test_data/germline_mutations/T1_test_mutation.tsv
• tests/test_data/output/T1_test.tsv

Annotate

Annotation of the PRMs is currently done semi-manually with Oncotator webserice. Perhaps at a later stage in development this will be done automatically. Missing is a VCF to Oncotator format converter.

Verify

Applies a given mutation in cDNA format to a transcript followed by the cDNA change of the PRM as predicted by Oncotator. Output gives a prediction of how the protein changes.

Run with:

revmut-verify tests/test_data/to_be_reverted_mutations.txt \
              tests/test_data/oncotator.ins.txt \
              tests/test_data/BRCA_transcripts.fa > tests/test_data/oncotator.ins.maf.out.tsv

View input/output files:

• tests/test_data/to_be_reverted_mutations.txt
• tests/test_data/oncotator.ins.txt
• tests/test_data/oncotator.ins.maf.out.tsv

Developers

Tests

In root dir run:

nosetests