Question: Regarding GATK pipeline
gravatar for aj123
5.0 years ago by
United States
aj12380 wrote:

Hello everyone- Im trying to set up a pipeline in GATK for variant analysis. I have human whole genome data, exome data and transcriptome data. I am also trying to look for overlaps in features (variants, gene mutations etc) in the 3 data sets. I would like any and all suggestions you would have on how to set up the pipeline and how to analyze this. Thank you for your help.

ADD COMMENTlink modified 5.0 years ago by Pierre Lindenbaum122k • written 5.0 years ago by aj12380

This is a question, not a tutorial. Also, there are many GATK-related answers here, all findable by search. For example:

A: Best Practices To Perform Exome Analysis (Illumina) Via Gatk

A: Getting A Large Vcf File On Variant Calling Through Gatk

ADD REPLYlink written 5.0 years ago by Alex Paciorkowski3.3k

I thought "type" meant what i was looking for, hence "tutorial"; but have removed that now. Thanks for pointing it out.

ADD REPLYlink written 5.0 years ago by aj12380
gravatar for Ashutosh Pandey
5.0 years ago by
Ashutosh Pandey11k wrote:

You can search this forum for related posts. A relevant post isĀ What Is The Best Pipeline For Human Whole Exome Sequencing?

ADD COMMENTlink written 5.0 years ago by Ashutosh Pandey11k
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