Enveomics collection

VCF.SNPs.rb

Counts the number of Single-Nucleotide Polymorphisms (SNPs) in a VCF file.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

VCF.SNPs.rb --input in_file [opts]

§ Arguments

Input*

 --input in_file  Input file in Variant Call Format (VCF).

Filtered VCF

 --out out_file  Output (filtered) file in Variant Call Format (VCF).

Min DP

 --min-dp integer  Minimum number of reads covering the position.

Max DP

 --max-dp integer  Maximum number of reads covering the position. By default no limit.

Min Ref-DP

 --min-ref-dp integer  Minimum number of reads supporting the REF allele.

Min Alt-DP

 --min-alt-dp integer  Minimum number of reads supporting the ALT allele.

Min quality

 --min-quality float  Minimum quality of the position mapping.

Min shannon

 --min-shannon integer  Minimum information content (in bits, from 0 to 1).

Indels

 --indels   Process indels.

* Mandatory.