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
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

picard MergeBamAlignment function require paired reads

qiangfuqiangfu BelgiumMember
edited January 2016 in Ask the GATK team

Does picard MergeBamAlignment function require paired reads as ALIGNED_BAM? This is not mentioned in the picard documents

However, we use trimmomatic to do reads QC, which generates three outputs: paired reads, unique reads after QC for 1st reads and 2nd reads. Then we use bwa to map three files individually to generate three sam files. Next, we merged bwa results into one bam file using picard MergeSamFiles. At last, we try to create a clean-up mapping file using picard MergeBamAlignment with a unmapped_bam file created from input fastq reads files using picard FastqToSam. The sort order of files are correct.

Does this mean picard and/or GATK does not work with a mixture of paired-reads and single-reads maps?

Best Answer


  • qiangfuqiangfu BelgiumMember

    I see. For our case, I will continue with only the paired reads in Trimmomatic result then. We will see in future whether we can skip Timmomatic step. Thanks for your time and help.

  • qiangfuqiangfu BelgiumMember
    edited February 8

    Are there any plan to change this? Now both bwa and bowtie2 can support mapping of both paired and single reads at the same time. And for some samples we are handling, it will be beneficiary if single reads can be handled together.

    Issue · Github
    by Sheila

    Issue Number
    Last Updated
    Closed By
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @qiangfu, there is no plan to change this as far as I'm aware. This is not a use case we have internally, and we can't justify the development time to do it given other more pressing priorities. If someone wants to implement this functionality and make a pull request to Picard, we could integrate it, of course.

Sign In or Register to comment.