rev-seqs 0.0.1

Revert sequences to consensus

rev-seqs: Revert Sequences to Consensus Preserving Variants

rev-seqs is a command line utility to revert sequences to consensus preserving variants detected in a VCF file. It reverts all other positions the sample consensus

Usage

Once installed rev-seqs is just a simple command line command.

python -m revseqs --input <input file> --vcf <vcf file> > <output_file>

run python revseqs -h for more options

The new bam file is written to standard output. Input file must be an indexed bam file

Inserts

Any inserts that are not flagged as variants are removed, those inserts along with sample header are printed to standard error. The sample name is followed by a comma separated list of insert positions that were removed.

To save this file for future inspect redirect standard error to a file using the command below

python -m revseqs --input <input.bam> --vcf <variants.vcf> > <output.bam> 2> <inserts>

Installation

pip install rev-seqs

Collaboration

If you have any issues, bugs, or feature requests please contact the author, [e-mail]