Cheripic
Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants (CHERIPIC), is a ruby tools to pick causative mutation from bulks segregant sequencing.
Currently this gem is still in development and nearing complete working package. And software only works with pileup as input files, use of bam and vcf files will be implemented in future
Installation
Cheripic is available both as a command line tool and as a gem.
Binaries are available for Linux 64bit and OSX.
Best way to use Cheripic is to download appropriate binary arhcive
unpack (tar -xzf) and add the unpacked directory to your PATH
Latest binaries are available to download here
To install gem and use the gem in your development
Add this line to your application's Gemfile:
gem 'cheripic'
And then execute:
$ bundle
Or install it yourself as:
$ gem install cheripic
Usage
Running cheripic without any input at command line interface shows following help options
Cheripic v1.2.0
Authors: Shyam Rallapalli and Dan MacLean
Description: Candidate mutation and closely linked marker selection for non reference genomes
Uses bulk segregant data from non-reference sequence genomes
Inputs:
1. Needs a reference fasta file of asssembly use for variant analysis
2. Pileup files for mutant (phenotype of interest) bulks and background (wildtype phenotype) bulks
3. If polyploid species, include of pileup from one or both parents
USAGE:
cheripic <options>
OPTIONS:
-f, --assembly=<s> Assembly file in FASTA format
-F, --input-format=<s> bulk and parent alignment file format types - set either pileup or bam (default: pileup)
-a, --mut-bulk=<s> Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1
-b, --bg-bulk=<s> Pileup or sorted BAM file alignments from background/wildtype bulk 2
--output=<s> Directory to store results, will be created if not existing (default: cheripic_results)
--loglevel=<s> Choose any one of "info / warn / debug" level for logs generated (default: debug)
--hmes-adjust=<f> factor added to snp count of each contig to adjust for hme score calculations (default: 0.5)
--htlow=<f> lower level for categorizing heterozygosity (default: 0.2)
--hthigh=<f> high level for categorizing heterozygosity (default: 0.9)
--mindepth=<i> minimum read depth to conisder a position for variant calls (default: 6)
--min-non-ref-count=<i> minimum read depth supporting non reference base at each position (default: 3)
--min-indel-count-support=<i> minimum read depth supporting an indel at each position (default: 3)
--ambiguous-ref-bases including variant at completely ambiguous bases in the reference
-q, --mapping-quality=<i> minimum mapping quality of read covering the position (default: 20)
-Q, --base-quality=<i> minimum base quality of bases covering the position (default: 15)
--noise=<f> praportion of reads for a variant to conisder as noise (default: 0.1)
--cross-type=<s> type of cross used to generated mapping population - back or out (default: back)
--use-all-contigs option to select all contigs or only contigs containing variants for analysis
--include-low-hmes option to include or discard variants from contigs with low hme-score or bfr score to list in the final output
--polyploidy Set if the data input is from polyploids
-p, --mut-parent=<s> Pileup or sorted BAM file alignments from mutant/trait of interest parent (default: )
-r, --bg-parent=<s> Pileup or sorted BAM file alignments from background/wildtype parent (default: )
--bfr-adjust=<f> factor added to hemi snp frequency of each parent to adjust for bfr calculations (default: 0.05)
--sel-seq-len=<i> sequence length to print from either side of selected variants (default: 50)
--examples shows some example commands with explanation
Example Commands
EXAMPLE COMMANDS:
1. cheripic -f assembly.fa -a mutbulk.pileup -b bgbulk.pileup --output=cheripic_output
2. cheripic --assembly assembly.fa --mut-bulk mutbulk.pileup --bg-bulk bgbulk.pileup
--mut-parent mutparent.pileup --bg-parent bgparent.pileup --polyploidy true --output cheripic_results
3. cheripic --assembly assembly.fa --mut-bulk mutbulk.pileup --bg-bulk bgbulk.pileup
--mut-parent mutparent.pileup --bg-parent bgparent.pileup --polyploidy true
--use-all-contigs true --include-low-hmes true --output cheripic_results
By default contigs with out a variant and thos contigs with lower scores are discarded.
so use options --no-only-frag-with-vars and --no-filter-out-low-hmes to disable them
Development
After checking out the repo, run bin/setup to install dependencies. Then, run rake test to run the tests. You can also run bin/console for an interactive prompt that will allow you to experiment.
To install this gem onto your local machine, run bundle exec rake install. To release a new version, update the version number in version.rb, and then run bundle exec rake release, which will create a git tag for the version, push git commits and tags, and push the .gem file to rubygems.org.
Contributing
Bug reports and pull requests are welcome on GitHub at https://github.com/shyamrallapalli/cheripic. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the Contributor Covenant code of conduct.
License
The gem is available as open source under the terms of the MIT License.