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!

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!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 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.

how to solve a problem with the depthofcoverage input format?

ge2sasagge2sasag Member Posts: 1

Hello, I´m trying to use deptofcoverage to check the coverage of my reads. I already have the indexed bam files (created with sam to bam) and also reordered (reorder SAM/BAM) but they are still not recognized by depthofcoverage and I got this error message:

"Sequences are not currently available for the specified build"

I used "human (homo sapiens) hg19 full" for mapping but I can´t select it, it only allows b37 version.

Any suggestions?

Thank you very much in advance

Gema

Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,163 admin

    Hi Gema,

    Are you using GATK via Galaxy? If so we can't help you, you'll need to ask the Galaxy support staff for help.

    If it turns out that you can't use hg19 via Galaxy, you should consider using command-line GATK instead. You will be able to use hg19, as well as a much more recent and improved version of the GATK tools.

    Geraldine Van der Auwera, PhD

  • ge2sasagge2sasag Member Posts: 1

    Hi! yes I´m using GATK through Galaxy, so I will ask them, thank you very much for your answer

    Best,
    Gema

Sign In or Register to comment.