search

jyhehir / mobster

For more details about Mobster please see
https://jyhehir.github.io/mobster/index.html
GNU General Public License v3.0
9 stars 9 forks source link

How to run mobster #5

Closed johanneskoester closed 7 years ago

johanneskoester commented 7 years ago

Dear @jyhehir, I am now trying to integrate mobster into our workflow, but I cannot find documentation how to run it. I have tried:

mobster -in ../data/LP6005615-DNA_G10.reheader.sorted.dedup.chr22.bam -out results/mobster/LP6005615-DNA_G10 -sn LP6005615-DNA_G10

but this gives me no log or error messages, and no output file at all...

jyhehir commented 7 years ago

Hi,

Strange that you have absolutely no error messages.

A typical way to run it would be

java -Xmx8G -jar MobileInsertions-0.2.1.jar -properties Mobster.properties -in A1_child.bam,A1_father.bam,A1_mother.bam -sn A1_child,A1_father,A1_mother -out A1_trio_mobster

I will update the build for the properties file.

Regards. Jayne

johanneskoester commented 7 years ago

Thanks!

jyhehir commented 7 years ago

version 0.2.2 provides many more resources required for Mobster, but you will still need to install Mosaik seperately. Please let me know if there are any more issues

johanneskoester commented 7 years ago

Thanks, I'll try!