Where can I find a sample analysis pipeline for DNA?
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?
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andrea •
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andrea •
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More examples of pipeline that you can extract some analysis are SpeedSeq, bcbio and IMPACT-pipeline.
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Hello, do you have only tumor sample or both tumor and normal?
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/