Where can I find a sample analysis pipeline for DNA?

Question

[andrea]

I want to learn how to develop a pipeline from data from TCGA or some other cancer genomics data. I know the general tools to use like picard and bwa. However, does someone have a good pipeline I can look at?

[noeD]

Hello, do you have only tumor sample or both tumor and normal?

[noeD]

some examples: https://software.broadinstitute.org/gatk/img/BP_somatic_workflow_M2.png http://gatkforums.broadinstitute.org/gatk/discussion/5963/tumor-normal-paired-exome-sequencing-pipeline https://www.nhlbi.nih.gov/research/intramural/researchers/core/systems-biology-core/services https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/

Answer 1

[geocarvalho]

More examples of pipeline that you can extract some analysis are SpeedSeq, bcbio and IMPACT-pipeline.