Dear All,

I have multiple name-sorted BAM files generated from pair-end DNA sequences which look like: R1-1.bam, R1-2.bam, ..., R2-1.bam, R2-2.bam, ..., and I am going to do SNP calling. Before SNP calling, I am not sure if I have to merge them together and then fill them in mate coordinates just like:

# Merge multiple name-sorted BAM files into one single BAM file. The option, -n,
# indicates the input files are sorted by read names rather than by chromosomal coordinates
samtools merge -n merged.bam *bam

# Fill the merged BAM file in mate coordinates
samtools fixmate -O bam merged.bam fixmated.bam

# Or piped above commands as
samtools merge - *bam | samtools fixmate -O bam - fixmated.bam

Could you please give me some comments or suggestions? Thank you in advance.

Best regards