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.
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.

☞ 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.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

picard MergeBamAlignment function require paired reads

BelgiumMember Posts: 7
edited January 2016

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?

Tagged:

• BelgiumMember Posts: 7

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.

• BelgiumMember Posts: 7
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 February 10 by Sheila

Issue Number
1731
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

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.

Geraldine Van der Auwera, PhD