compare-snps
$program_version
Compare two or more files containing regulatory SNPs (predicted or annotated).
Regulatory SNPs can be obtained from a variety of sources:
variation-scan
RSAT program that predicts rSNPs by scanning SNP sequences with position-specific scoring matrices.
is-rsnp
A Web site allowing to predict rSNPs or to retrieve pre-computed predictions.
http://bioinformatics.research.nicta.com.au/software/is-rsnp/
haploreg
A web site combining annotations and predictions of regulatory SNPs, as well as integration of SNPs with regulatory information (ChIP-seq for transcription factors, histone modifications, …).
compare-snps \[-i inputfile\] \[-o outputfile\] \[-v #\] \[...\]
The output format is a tab-delimited file, with one row per rSNP.
A regulatory SNP is defined by 2 mandatory fields:
SNP ID
The identifier of the SNP shown or predicted to affect regulation.
TFBM
Identifier of the transcription factor binding motif (TFBM) affected by the SNP.
variation-scan
The program compare-rsnps takes as input the results of variation-scan.
-v #
Level of verbosity (detail in the warning messages during execution)
-h
Display full help message
-help
Same as -h
-i inputfile
If no input file is specified, the standard input is used. This allows to use the command within a pipe.
-o outputfile
If no output file is specified, the standard output is used. This allows to use the command within a pipe.