a ruby tools to pick causative mutation from bulks segregant sequencing
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README.md

Cheripic

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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 v1.2.6
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/Bam files for mutant (phenotype of interest) bulks and background (wildtype phenotype) bulks
3. If providing bam files, you have to include vcf files for the respective bulks
4. If polyploid species, include pileup/bam files 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 or vcf (default: pileup)
  -a, --mut-bulk=<s>               Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1
  --mut-bulk-vcf=<s>               vcf file for variants from mutant/trait of interest bulk 1 (default: )
  -b, --bg-bulk=<s>                Pileup or sorted BAM file alignments from background/wildtype bulk 2
  --bg-bulk-vcf=<s>                vcf file for variants from background/wildtype bulk 2 (default: )
  --output=<s>                     custom name tag to include in the output file name (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 at a position to consider for variant calls (default: 6)
  --max-d-multiple=<i>             multiplication factor for average coverage to calculate maximum read coverage
                                   if set zero no calculation will be made from bam file.
                                   setting this value will override user set max depth (Default: 5)
  --maxdepth=<i>                   maximum read depth at a position to consider for variant calls
                                   if set to zero no user max depth will be used (default: 0)
  --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=<s>        including variant at completely ambiguous bases in the reference (default: false)
  -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=<s>            option to select all contigs or only contigs containing variants for analysis (default: false)
  --include-low-hmes=<s>           option to include or discard variants from contigs with
                                   low hme-score or bfr score to list in the final output (default: false)
  --polyploidy=<s>                 Set if the data input is from polyploids (default: false)
  -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: )
  -R, --repeats-file=<s>           repeat masker output file for the assembly  (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.