Regarding GATK pipeline
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.
1 answer
You can search this forum for related posts. A relevant post is What Is The Best Pipeline For Human Whole Exome Sequencing?
• 0 views
•
link
updated
by
Ram
•
written
by
Ashutosh Pandey
•
written
by
Ashutosh Pandey
Log in to answer this question.
More posts like this
-
How to extract and analyze variant sequences from gnomAD v4 exome VCF
written by Rohan •
-
Seeking Opinions on Pipeline for Detecting Somatic Variants and Rare Germline Mutations
written by George •
-
VarDict in paired end mode with GATK preprocessing
written by kulvait
-
how to annotate variants to human reference genome in R
written by pt.taklifi
-
Correlation between coverage and variant calling
written by vinayjrao
-
How to get unique somatic mutations for each individual patients
written by vivekruhela •
-
EGFR and KRAS expression
written by aj123
-
How do you validate called SNPs from NGS data?
written by mattbawn •
-
Tools For De Novo Assembly For Exome Sequencing Data
written by michealsmith
-
Is Post Filtering Of Vqsr Calls Necessary With Gatk?
written by User 1666 •
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.