I want to do GATK variant calling. I have several raw-paired-end-reads fastq files for one pig individual. And I have finished mapping using bwa mem. GATK best practices (for calling germline SNPs + indels) tells that after mapping, I need to merge bam files. And it recommends
picard MergeBamAlignment. what's the difference between
picard MergeBamAlignment and
samtools merge please? I found the input files they need are different. The former one need unmapped bam file as well as the reference genome file. And in my understanding, each
MergeBamAlignment command is only for one fastq (pair) file, not for multiple fastq files. Is there any other difference please? Particularly, are their aims, and their output results any different please? I feel that
MergeBamAlignment is for combining the information both from mapped file and unmapped file. samtools merge is for combining diffferent mapped file into one big mapped file. Or Can I ignore GATK's advice and simply use
samtools merge instead? Thank you.