Required arguement in MergeBamAlignment

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Shvartsman

• November 16, 2023 06:46

I try to impliment 'gatk MergeBamAlignment', it required three arguments in description: output file, reference sequence and unmapped bam file. I enter the next command: ./miniconda3/pkgs/gatk4-4.2.3.0-hdfd78af_1/bin/gatk MergeBamAlignment -O ./exp/2step -R ./references/Homo_sapiens/hg38.fa -UNMAPPED_BAM ./exp/1step/lv_1u.bam. But it returns: Either ALIGNED_BAM or the combination of READ1_ALIGNED_BAM and READ2_ALIGNED_BAM must be supplied. Tool returned: 1 I can not understand why aligned_bam is required. Which is algorithem of recieving such bam-file?

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  Gökalp Çelik

  • November 16, 2023 19:44

  Hi Shvartsman

  Looks like arguments page for the tool is missing another required input which is the aligned bam file. This tool takes one unaligned and one aligned bam file to merge as one bam file with added tags and marks from the unaligned bam file. 

  We will fix this issue and reflect the required parameter Alignment Bam file. 

  Regards. 

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