Error when viewing a bam file

Question

[Chris]

Hi all, would you please tell me what is wrong in this case? Thank you.

samtools view Library_allAligned.out.bam | head -n 10
[main_samview] fail to read the header from "Library_allAligned.out.bam"

[GenoMax]

Your BAM file may be missing a header. Do you see anything if you do samtools view -H Library_allAligned.out.bam?

[Chris]

No. I got the same error.

[GenoMax]

How did you make the BAM?

[Chris]

I used STAR. This is whole genome data with 2 libraries. I guess the error is because I merge two bam files.

[GenoMax]

Can you run the view -H command on the two original files? Merging should preserve the header unless you tried to merge files aligned to two different genomes.

[Chris]

Yes, view -H worked on the two original files. I used the same reference genome. Would you please suggest what wrong in this case? I sorted before merging.

samtools merge finalBamFile2.bam sorted_sample1.bam sorted_sample2.bam

[GenoMax]

Can you try?

samtools merge -h file1.bam -o merged.bam file1.bam file2.bam

[Chris]

I am running your command. The first bam file is light but the second is 66 Gb so I took quite a long time to finish. Do you think using batch submit with more CPU makes it finish faster?

[GenoMax]

merge command can use multiple threads and will also write out an index.

-@, --threads INT
               Number of additional threads to use [0]
      --write-index
               Automatically index the output files [off]

[Chris]

So the command will be something like:

samtools merge --threads 2 --write-index -h file1.bam -o merged.bam file1.bam file2.bam

Is that correct?