Merging bam files

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9.0 years ago

jyu429 ▴ 120

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?

bam merge • 3.2k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 9.0 years ago by jyu429 ▴ 120

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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.

ADD REPLY • link 9.0 years ago by Devon Ryan 104k

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

ADD REPLY • link updated 5.0 years ago by Ram 44k • written 9.0 years ago by mkulecka ▴ 360

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

ADD REPLY • link 9.0 years ago by Devon Ryan 104k

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What version are you using?

ADD REPLY • link 9.0 years ago by Devon Ryan 104k

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Version 1.1. Is that too outdated?

ADD REPLY • link 9.0 years ago by jyu429 ▴ 120

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

ADD REPLY • link 9.0 years ago by Devon Ryan 104k

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I updated it and it gives me the same error.

ADD REPLY • link updated 5.0 years ago by Ram 44k • written 9.0 years ago by jyu429 ▴ 120

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