HyperMut

Hyper mutation detection program to identify sequences that have multiple T-to-C or G-to-A mutations in a fragment.

Primary inputs are a sam file and a reference sequence. This program have several configurable parameters including the quality threshold, maximum number of undetermined nucleotides, threshold to count as "many" mutations, and specify the range of sequence that should be considered and ignored due to PCR primers.

An example would look like:

  ruby sammmcontext-f4.rb --ref=ref.fa --sam=sample.sam \
    --min-qv=60 --max-N=3 -m 600 -t 2 \
    -p 1 -e 4264 -c 27 -d 4246 -g 3699 -h 3911 \
    > sample.ref.highsubstcuorga.out60c

See the program for detail of the parameters.

While sammmcontext-f4.rb assumes paired overlapping reads and seek mutation on the consensus, sammmcontext-s.rb works with single read.