Merging bam files

Question

[jyu429]

Hi, I'm trying to merge these two bam files and I did the command

samtools merge merged.bam file1.bam file2.bam

However, it gives me this error:

[trans_tbl_init] @SQ SN (hg38_gold start=chr14:105786368 strand=+) found in binary header but not text header.

I'm not sure how to get around this. Is there an option I need to turn on to suppress/fix this?

[Devon Ryan]

I just checked the code. This should happen whenever you have a chromosome missing between the files that you want to merge. You might be able to get around this with samtool merge merged.bam file2.bam file1.bam, but if not then it makes sense to reheader at least one of the files to have all of the chromosomes (put the missing ones at the end, don't change the order of any of the existing ones!) and then merge.

[mkulecka]

Or you can try MergeSamFiles commans from picard tools. It is better in handling headers than samtools.

[Devon Ryan]

Indeed, picard tends to be a bit friendlier with merging headers.

[Devon Ryan]

What version are you using?

[jyu429]

Version 1.1. Is that too outdated?

[Devon Ryan]

Can you update to 1.2 and see if that fixes it?

[jyu429]

I updated it and it gives me the same error.