mutspec_filter.md

MutSpec-Filter (optional)

Filter out variants that are likely neutral polymorphisms using Annovar annotations (dbSNP, ESP...) or additional databases in VCF or BED format.

Input format

Tab delimited text files generated by MutSpec-Annot.

Output

Tab delimited text file filtered for variants considered as neutral polymorphisms.

Usage

perl mutspecFilter.pl --thG --filter bed1 --filter bed2 --refGenome hg19 --pathAVDBList mutspec/hg19_listAVDB.txt --outfile output_filename input_file

List of parameters:

Parameter	Default value	Description
--dbSNP	0	Column number for dbSNP (start to count from 1)
--segDup	false	Remove variants present at >= 0.9 frequency in the genomic duplicate segments database
--esp	false	Remove variants present at frequency > 0.001 in the Exome Sequencing Project database (only valid for human genomes)
--thG	false	Remove variants present at frequency > 0.001 in the 1000 genome database (only valid for human genomes)
--exac	false	Remove variants present at frequency > 0.001 in the EXome Agregate Consortium database (only valid for human genomes)
--filter		Path to one VCF or BED file to filter against (Multiples --filter are allowed)
input		Input file to filter
--outfile		Path to output file
--help		Print help message