Other functions

Genome region operations

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

Primer design

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