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Makeprimers

Format

cg makeprimers regionfile maxsize prefsize dbdir ?minfreq? ?threads?

Summary

Make sequencing primers for Sanger validation experiments

Description

This command makes primers for sequencing target regions of the genome. It will try to avoid having known SNPs (from dbSNP) or repeats in the primers. If these canot be avoided, it will annotate the primers with this info. Variants close together can be grouped into regions first using the command:

cg makeregions selvariantlist.tsv 200 > regionfile.tsv

Arguments

regionfile

tsv that has at least the columns chromosome, begin, end; must be sorted by chromosome, then begin

maxsize

the maximum amplicon size

prefsize

the prefered amplicon size

dbdir

directory containing reference genomes, region and variation data

minfreq

only snps with a frequency > minfreq will be avoided. All will be used if minfreq is not given or smaller than 0

threads

how many threads to use (use 1)

Category

Validation