Question

Where can I find a sample analysis pipeline for DNA?

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7.0 years ago

andrea • 0

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?

next-gen WES WGS SNP sequencing • 1.6k views

ADD COMMENT • link updated 7.0 years ago by geocarvalho ▴ 360 • written 7.0 years ago by andrea • 0

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

ADD REPLY • link 7.0 years ago by noeD ▴ 130

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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/

ADD REPLY • link 7.0 years ago by noeD ▴ 130

score 1 · Answer 1 · 2017-04-13

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7.0 years ago

geocarvalho ▴ 360

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

ADD COMMENT • link 7.0 years ago by geocarvalho ▴ 360