You can follow my NGS tools from docker hub keyword skysbiodocker.
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- Gökalp Çelik
If you do not want to mess with your system settings or if you are unable to do that due to lack of privileges you may modify the bellow line in gatk script return ["java"] + PACKAGED_LOCAL… (View Post)6 · Share on Google+
As far as I remember there is a filter for mapping quality for readcounts as well as there is an additional step for filtering where depth shows massive variability among the samples in the overall f… (View Post)2 · Share on Google+
Is it possible that there are multiple read groups in there with the multiple sample names such as lane numbers? Can you check/post the header of the bam file? (View Post)
What is your code for creating seperate imports? Maybe there is something fishy going on there.. (View Post)