Can ART be used to generate a WES .sam file rather than a WGS file?
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2.2 years ago
K.patel5 ▴ 150

Dear biostars,

I am generating some synthetic sequencing files to benchmark my WES based CNV detection pipeline. I have generated a synthetic genome with simuG and am generating synthetic read files using ART with the code below.

art_illumina -ss HS20 -sam -i $genome -p -l 100 -f 20 -m 150 -s 10 -ir -dr -o $name

This creates a very detailed genome, but is there a way I can adjust the parameters to generate WES data instead?

Also does anyone have any advice on how to use ART in a way to generate more sporadic read depths across the genome? This would better simulate the quality of real-world data I am benchmarking by CNV detection pipeline for.

Cheers

genomics biology WGS synthetic WES • 408 views
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