NAME

locate_SNPs.pl

A script to locate the position of SNPs and identify codon changes.

SYNOPSIS

locate_SNPs.pl --db <database> <snp_file1> ...
 
 Options:
 --in <snp_file>
 --db <database>
 --features type1,type2,...
 --version
 --help

OPTIONS

The command line flags and descriptions:

--in <snp_file>

Specify the name(s) of the input SNP file(s). SNP files should be in the Variation Call Format (VCF) format. They may be gzipped. Multiple files may be specified; they will be processed sequentially. Provide multiple --in arguments, a comma delimited list, or a free list at the end of the command.

--db <database>

Specify the name of a Bio::DB::SeqFeature::Store annotation database from which gene or feature annotation may be derived. For more information about using annotation databases, see https://code.google.com/p/biotoolbox/wiki/WorkingWithDatabases.

--features type1,type2,...

Provide a comma-delimited list (no spaces) of the GFF3 feature types of the features to intersect with the SNPs. Complex gene structures (gene->mRNA->CDS) can be parsed to look for amino-acid changes. The default feature is "gene".

--version

Print the version number.

--help

This help text.

DESCRIPTION

This program will locate SNPs and other sequence variants and identify the feature that overlaps the variant. In most cases, the features are genes, in which case the corresponding coding sequence (CDS), if present, is evaluated for a change in coding potential due to the sequence variation. Codon changes, silent changes, and frame shifts may be reported.

The input SNP files must be in the Variant Call Format (VCF) 4.0 or 4.1 format, a tab-delimited text file with metadata. See http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 for more information about the format. The files may be gzipped.

Numerous SNP callers are capable of generating the VCF format from sequence (usually Bam) files. The Samtools program is one such program, using the "mpileup" function in conjunction with it's "bcftools" tool. See the Samtools site at http://samtools.sourceforge.net for more information.

The output file is a simple tab-delimited text file with headers, suitable for opening in spread-sheet program. Each row represents a SNP. The following columns are include.

Variation_Type (substitution, insertion, deletion)
Overlapping_Feature (feature type, name, alias)
Subfeature (exon, CDS, etc)
Codon_Change (Reference AA -> mutant AA)
Chromosome
Position (start position, 1-base, forward strand)
Reference_Seq
Variant_Seq
Number_Supporting_Reads (if reported)
Total_Number_Reads (if reported)
Percent_Supporting_Reads (if reported)
Genotype (if reported)
Feature_description (if present in the database)

If more than one variant sequence is reported at a position, then each is evaluated for effects on the coding potential. If more than one feature is found overlapping the SNP, then both features are reported.

AUTHOR

Timothy J. Parnell, PhD
Dept of Oncological Sciences
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112

This package is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0.