The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Picard 2.9.4 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

Problem with GATK pipeline, merging VCF and ped file.

Hi to all

I have just started using GATK and I have few question about some tools and about the general workflow.

I have 3 exome-seq data from a trio and I have to detect rare or private variants that segregate with the disease.

From the 3 aligned bam file I procedeed with the GATK pipeline (ADDgroupInfo, MarkDup, Realign, BQSR, Unified Genotyper and variant filtration) and I generated 3 VCF file.

As now I have to use the PhaseByTrasmission tool, should I merge the 3 VCF file?

Or it was better to merge the BAM file after adding the group info and proceed with the other analysis?

And should I create my .ped file,(I visited http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped, but I couln't understand how ped file is generated) based on the read group that I have assigned?

Thanks!!!

Best Answer

Answers

Sign In or Register to comment.