Merging multiple BAM files

[unibegenomics]

Hello all,

We are new to using samtools and are trying to solve a problem with merging multiple BAM files.

We have several BAM files, one from each individual. They have all been mapped (one at a time) to the same reference genome, whose assembly consists of about 7000 scaffolds. Now reads from each individual map to several but not always all of the scaffolds in the reference. Therefore, for example, individual_1 may have no reads mapping to scaffold 1234 of the reference, but individual_2 might. Now we want to merge all of these alignments into a single BAM file but samtools cannot deal with the fact that some scaffold names do not match.

The BAM files were created using samtools from SAM files exported from CLC genomics workbench.

Any help will be greatly appreciated.

Thanks.

[sdvie]

I am not familiar with the importance of scaffolds in the reference genome.

However, I would recommend to try and use picard tools.
It does things similar to samtools and more.

Perform two steps:

1. AddAndReplaceReadgroups for each of your bam files (to annotate the reads and be able to follow them in the merged file).
2. MergeSamFiles. Although the tools says "sam", it also works for bam files.

good luck!