search

cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
57 stars 20 forks source link

depth parameter #74

Closed gbnci closed 6 years ago

gbnci commented 6 years ago

I have tried to run brass.pl but get error like: "Option 'depth' has not been defined". Not quite sure what I should put there. Should I put number like "-d ###", or file "-d file", if it is file, what file, bas file? I have bas file generated in the same directory. Here is the command line: brass.pl -o outfolder -t tumor.bam -n normal.bam -r genome.fa; the names of bas files are tumor.bam.bas and normal.bam.bas . Any suggestions would be appreciated. Yonghong Wang

AndyMenzies commented 6 years ago

The depth option takes a file. Have a look at the BRASS wiki here on github, it details how to obtain or generate the inputs.