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.

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
Picard 2.10.2 is now available at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

ReduceReads parallelism

aihardinaihardin Member
edited August 2012 in Ask the GATK team

I'm working with ReduceReads and would like to use it in some kind of parallel mode. The presentation mentions that a 50x way run may drastically reduce run time but I'm not sure how to invoke this. I tried -nt and it complained. Should I be giving it multiple intervals and merging? If so, how does it deal with edge variants?

Thanks.

Best Answer

  • CarneiroCarneiro Charlestown, MAMember
    Accepted Answer

    Yes, you need to run non overlapping (farther than read length apart) intervals independently and merge the results together.

    -nt is incompatible with Read Walkers, unfortunately.

Answers

  • CarneiroCarneiro Charlestown, MAMember
    Accepted Answer

    Yes, you need to run non overlapping (farther than read length apart) intervals independently and merge the results together.

    -nt is incompatible with Read Walkers, unfortunately.

Sign In or Register to comment.