samtools merge

[bair]

I'm going to merge > 50 alignment bam files (is it possible to merge this number of bam files?), it's too big,
thus I want to merge by chromosome.

1. samtools view -u file1.bam chr1 > chr1.file1.bam
2. samtools view -u file2.bam chr1 > chr1.file2.bam

no problem to create the above two files.

3. samtools merge chr1.bam chr1.file1.bam chr1.bam


[bam_header_read] EOF marker is absent.


Since the merged file looks ok,

What does this information mean?

thanks

[lh3]

It means either a) you BAM is generated by an old version of samtools; or b) your BAM is truncated.

[bair]

Originally Posted by lh3

It means either a) you BAM is generated by an old version of samtools; or b) your BAM is truncated.

I uased bowtie for alignment, and convert it's sam output to bam by samtools.

Thanks.

[rahilsethi]

Hi,

I am having the same problem as blair had when used samtools merge:

[bam_header_read] EOF marker is absent. The input is probably truncated.

I also followed the same steps

1. Files: bam1_sorted_indexed.bam, bam2_sorted_indexed.bam
2. Merge: samtools merge -u output.bam bam1_sorted.bam bam2_sorted.bam

Merge files with no problem, but further running samtools on merged bam file such as samtools sort or samtools depth gives the above "EOF marker absent" warning, though it does produce the output.

When using Picard I did not have such problem, but Picard seems to be not able to handle large eg. if bam1 >= 8G or bam2 >= 8G, where it breaks and gives runtime error. In those cases one might have to rely on samtools merge. Should I be concerned about the above warning samtools gives?

[rahilsethi]

to add to the above
a) my bam files are generated by the same samtools version as the merged file and also for the sort and depth activities (0.1.18)
b) my bam files are also not truncated since Picard can run fine

[swbarnes2]

It might be the -u in your command line.

If you do something like this:

samtools view -bShu file.sam > file.bam
samtools sort file.bam sort

samtools will complain that there is no EOF marker. But it still works fine.