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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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allow use of BED file for manifest #34

Open alanhoyle opened 7 years ago

alanhoyle commented 7 years ago

We're using custom targeted sequencing from a different company than Illumina. They don't provide us with a Nextera manifest formatted file, but I was able to get things to run and get some results by performing some editing, and awk/perl/etc. to make a file that at least looks like an example manifest file I've seen online. It would be much easier to deal with if the --manifest parameter could accept a standard BED file in addition to the proprietary Nextera Manifest format.

chihlee commented 7 years ago

This is certainly possible. @eroller I guess we can add it to our backlog.

Steve

eroller commented 7 years ago

Yes, this would be a nice feature and I have added to our backlog. We are happy to take a pull request if you want to get this feature in sooner.

brendanofallon commented 7 years ago

Any word on this? Seems like an important feature, BED is the format used by (I think) every other CNV caller, would be a shame not to support it.

MatthewPorterGN commented 7 years ago

+1, we would like to use this tool for T/N but BED format is the near-universal standard we have seen used for region reporting.

BenoitFiset commented 6 years ago

Is the BED file option now available ? Or still have to do a session of awk / sed / perl -pe ?

eroller commented 6 years ago

A bed option is still not available. We haven't updated our Enrichment workflow as we are focusing on WGS.