noflag option still requires flagging files

cancerit / cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis

http://cancerit.github.io/cgpCaVEManWrapper/

GNU Affero General Public License v3.0

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Closed ghost closed 7 years ago

ghost commented 7 years ago

Even with the noflag option we are testing for VCF unmatched folder and germline indels...

keiranmraine commented 7 years ago

for germline indel with WXS analysis I've been using:

echo '#comment' >  $TMP/empty.germline.bed