The current GATK version is 3.8-0
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.

Got a problem?

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
Download the latest Picard release at
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

UG/HC interval list running start

GATK Team:

This comment came up after some discussion with a colleague of mine:

"If you split the human genome into 100 pieces, we have to create overlapping regions so that GATK won't miss variants, but this creates a complicated situation where you may have to merge variants at the same locus."

Is it true that I would have to pad intervals and explicitly resolve variants (if called at the same locus)? If I use -L target_intervals specifying non-overlapping intervals, does GATK get a "running start" (say 50bp upstream to get variant context) before emitting variants--as samtools mpileup/bcftools claims to--or does GATK jump in directly at the start of the specified interval (and may not then call variants within some short starting interval)?

Your clarification would be much appreciated.

Best Answer


Sign In or Register to comment.