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picard MergeBamAlignment function require paired reads

qiangfuqiangfu BelgiumMember Posts: 7
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 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.

  • qiangfuqiangfu 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
    by Sheila

    Issue Number
    Last Updated
    Closed By
  • Geraldine_VdAuweraGeraldine_VdAuwera Administrator, Dev Posts: 11,118 admin

    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

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