What order should the process be executed in python？

[pancratm]

I'm new to here.
I have read the paper (Genomic data analysis workflows……）and want to execute the pipeline with your python code. Can you please tell me the order of these python files(read_group_from_fastq.py,filter_trim.py,filter_dna_coverage)?

[gbeane]

I assume you are trying to execute this pipeline without using the Civet framework?

Each Civet pipeline has an XML flie that describes the execution flow of the pipeline. This will be the XML file with the outer tag (for example, RNA_PDX/XenomeRnaSeqSingleSamplePE.xml). You'll need to look at this file to determine which order the tools are called.

[pancratm]

Thanks a lot!
Acutually I just want to know the step of how to filter the germline variants. I read the paper and knew the step needs four databases three of which are open. Would the mutation both in acquired germline mutation and our findings from previous steps be deleted directly? Or can you tell me which function in GATK would be used in the step?
Thanks.

[xingyi19]

germline variants are not deleted. they should only be flagged if they are present in the databases.

[xingyi19]

Variant annotation xml have commands from snpeff and snpsift for annotation of various databases.