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Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
What is the GATKReport file format?
A GATKReport is simply a text document that contains well-formatted, easy to read representation of some tabular data. Many GATK tools output their results as GATKReports, so it's important to understand how they are formatted and how you can use them in further analyses.
Here's a simple example:
#:GATKReport.v1.0:2 #:GATKTable:true:2:9:%.18E:%.15f:; #:GATKTable:ErrorRatePerCycle:The error rate per sequenced position in the reads cycle errorrate.61PA8.7 qualavg.61PA8.7 0 7.451835696110506E-3 25.474613284804366 1 2.362777171937477E-3 29.844949954504095 2 9.087604507451836E-4 32.875909752547310 3 5.452562704471102E-4 34.498999090081895 4 9.087604507451836E-4 35.148316651501370 5 5.452562704471102E-4 36.072234352256190 6 5.452562704471102E-4 36.121724890829700 7 5.452562704471102E-4 36.191048034934500 8 5.452562704471102E-4 36.003457059679770 #:GATKTable:false:2:3:%s:%c:; #:GATKTable:TableName:Description key column 1:1000 T 1:1001 A 1:1002 C
This report contains two individual GATK report tables. Every table begins with a header for its metadata and then a header for its name and description. The next row contains the column names followed by the data.
We provide an R library called
gsalib that allows you to load GATKReport files into R for further analysis. Here are four simple steps to getting
gsalib, installing it and loading a report.
1. Start R (or open RStudio)
$ R R version 2.11.0 (2010-04-22) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.
2. Get the
gsalib library from CRAN
gsalib library is available on the Comprehensive R Archive Network, so you can just do:
From within R (we use RStudio for convenience).
In some cases you need to explicitly tell R where to find the library; you can do this as follows:
$ cat .Rprofile .libPaths("/path/to/Sting/R/")
3. Load the gsalib library
4. Finally, load the GATKReport file and have fun
> d = gsa.read.gatkreport("/path/to/my.gatkreport") > summary(d) Length Class Mode CountVariants 27 data.frame list CompOverlap 13 data.frame list