GenomeComb
Genomecomb moved to github on https://github.com/derijkp/genomecomb with documentation on https://derijkp.github.io/genomecomb. For up to date versions, go there. These pages only remain here for the data on the older scientific application (or if someone really needs a long obsolete version of the software)
Some examples of operations on genome regions files. Although some of the operations can also be achieved by advanced queries, we show here how to use regions files.
Select regions sequenced by CG (with two SNV callers)
cg select -q 'count($sequenced-cg*, == 1) == 4' \
NA19240_chrom22.tsv.gz > reg_2.tsv
Then calculate how large the selected regions are
cg covered reg2.tsv > reg2.covered
Select regions representing all missense SNVs
cg select -q '$impact =="MISSENSE" && $type == "snp" ' \
NA19240_chrom22.tsv.gz > reg_missense.tsv
Join both region files
cg regjoin reg_2.tsv reg_missense.tsv > joined.tsv
Subtract missense SNVs from the first file
cg regsubtract reg_2.tsv reg_missense.tsv > subtracted.tsv
First select regions for design for all missense SNVs
cg makeregions reg_missense.tsv 200 > regval_missense.tsv
Then make primers for them using the experiment name ValidationName and the location of the reference genome
cg makeprimers regval_missense.tsv ValidationName 600 500 dbdir > primers-valreg.tsv