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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?