Error when viewing a bam file
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13 months ago
Chris ▴ 290

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"
samtools • 905 views
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Your BAM file may be missing a header. Do you see anything if you do samtools view -H Library_allAligned.out.bam?

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No. I got the same error.

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How did you make the BAM?

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

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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.

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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
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Can you try?

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

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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]
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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?

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