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 2.9.0 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.

limitation in command length

naarkhoonaarkhoo Member Posts: 38

I wonder if there is any limitation for the command length.
I provide more than 90 bam files, including their directory address to GATK for variant calling using UnifiedGenotyper, and it seems it doesn't parse whole the command.
I know It could be because of java, also. Have you ever experiences similar problem ?
Is there any way to provide a directory path instead of all single bam files path as the input ?
thanks,

Best Answer

Answers

  • naarkhoonaarkhoo Member Posts: 38

    I don't know if it is relevant but it complains about un-index bam files.
    Should all bai files (indeces) located in the same directory ? is there option to set the path of bai files also?

  • naarkhoonaarkhoo Member Posts: 38

    Or to know which of the listed BAM files is not index-ed

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,669 admin

    Yes, the bai file indices should be in the same directory as the bams they index. There is no option to provide separate paths for the bam and bai.

    Geraldine Van der Auwera, PhD

Sign In or Register to comment.