bam file merge

Question

[genomics Newbie]

Hello. I have numerous bam files which I need to merge into a single bam file. How do I know whether I need to first index and sort the bam files?

[tiago211287]

In http://www.htslib.org/doc/samtools-1.2.html, it says,

-h is specified the @SQ headers of input files will be merged into the specified header, otherwise they will be merged into a composite header created from the input headers. If in the process of merging @SQ lines for coordinate sorted input files, a conflict arises as to the order (for example input1.bam has @SQ for a,b,c and input2.bam has b,a,c) then the resulting output file will need to be re-sorted back into coordinate order.

[Farbod]

Dear genomics Newbie, Hi

Please have a look at To sort or not to Sort?.

I guess you can first use "samtools merge" and then "samtools sort -o".

Answer 1

[h.mon]

You should sort your files, as samtools merge expects sorted bam files, either by position (default) or by name (samtools merge -n). You can check if you bam are already sorted by looking at the SO flag:

samtools view -H file.bam | grep "SO:"

@HD VN:1.0 SO:coordinate