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,
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