GenomeComb

sam_clipamplicons

Format

cg sam_clipamplicons ampliconsfile file outfile

Summary

Clip primers from aligned sequences in a sam file (by changing bases to N and quality to 0) given a set of target amplicons

Description

Arguments

ampliconsfile
tab delimited file containing targets with at least following columns: chromosome begin end
file
directory containing reference genomes and variation data
outfile
directory containing reference genomes and variation data

Category

Process