Merging BAM files before sorting

[tahamasoodi]

Hi,

I have multiple BAM files of the same sample from 2 different runs. Do I first merge these and then later do sorting or the otherway? I heard someone say that we must first do coordinate sorting for each BAM file and then merge the sorted files. Does it make difference?

Thanks

[dpryan]

It doesn't matter if you sort and merge or merge and sort, you'll get the same result either way. BTW, instead of using "samtools merge", use "samtools cat" (you're going to subsequently sort them anyway).

[tahamasoodi]

Thanks! I've already used samtools merge for previous samples, what difference samtools cat will do? Will it decrease the processing time?

[dpryan]

Yeah, it'll just make things a bit faster. Merge is only needed if you need to keep a sorting order constant, but if you're going to sort things after the fact anyway then there's no point.