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 https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

Reduced Bam hangs in Crest

sheenamssheenams Member
edited January 2013 in Ask the GATK team

I've tried using the output of the Reduced Bams as an input to Crest (after some preprocessing) but it hangs on chr7. Has anyone else used the reduced bam in other programs? Is this output meant to only be used in GATK?

Thanks!

Post edited by Geraldine_VdAuwera on
Tagged:

Best Answer

  • CarneiroCarneiro Charlestown, MAMember
    Accepted Answer

    I don't know what Crest is, but the reduced BAM, although a valid BAM, may crash programs that are not expecting extremely large reads. I suggest you contact the Crest developers with this bug report.

Answers

  • CarneiroCarneiro Charlestown, MAMember
    Accepted Answer

    I don't know what Crest is, but the reduced BAM, although a valid BAM, may crash programs that are not expecting extremely large reads. I suggest you contact the Crest developers with this bug report.

Sign In or Register to comment.