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cbg-ethz / NGS-pipe

NGS-pipe: next-generation sequencing pipelines for precision oncology
Apache License 2.0
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No example for WGS data #25

Open readbio opened 6 years ago

readbio commented 6 years ago

Thanks for developing this nice pipeline. I'm trying to use it for WGS data. In the wiki page (https://github.com/cbg-ethz/NGS-pipe/wiki/Installation-&-Testing), I saw the the command lines for WGS data. But I didn't find the corresponding files in the example folder: examples/dna. Could you please add it? Thanks again.

singerj commented 6 years ago

Hi,

We will include a working example for WGS data, however, this will take some time. In the meantime, the WES example can be used for variant calling. If applied to WGS data, the only difference is the regions file (which should simply include all positions of all chromosomes) that has to be changed in the config.json file.

Best, Jochen