Entering edit mode
9.6 years ago
aj123
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120
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.
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
I thought "type" meant what i was looking for, hence "tutorial"; but have removed that now. Thanks for pointing it out.