[Samtools-help] Merge and fixmate of multiple BAM files generated from pair-end DNA sequences

[Lisa D. <lis...@ya...>]

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 coordinatessamtools merge –n merged.bam *bam # Fill the merged BAM file in mate coordinatessamtools fixmate -O bam merged.bam fixmated.bam # Or piped above commands assamtools merge - *bam | samtools fixmate -O bam - fixmaated.bam Could you please give me some comments or suggestions? Thank you in advance. Best regards,