samtools mpileup's options -b (more than one bam file) and -r cannot be used together

Question

[jing.mengrabbit]

Hi, I would like to generate a mpileup file from 2 bam files in some regions instead of the whole chromosomes:

samtools -b bam_list_file -r regions_to_be_parsed.bed > mpileup_from_two_bam_files.pileup

The content in the bam_list_file is

~/1.bam

~/2.bam

but an error was given:

[E::mpileup] fail to parse region 'regions_to_be_parsed.bed' with 1.bam.

I do not think there is something wrong with the bam files or the bed file, because it works when I ran with the following command:

samtools -r regions_to_be_parsed.bed ~/1.bam > mpile1.pileup

samtools -r regions_to_be_parsed.bed ~/2.bam > mpile2.pileup

samtools -b bam_list_file > mpileup_from_two_bam_files.pileup

Is there some way to generate a mpileup file from two bam files with regions in bed file? Thanks for your time!

[h.mon]

Hello jing.mengrabbit,

Please use the formatting bar (especially the code option) to present your post better.

For example:

samtools -b bam_list_file -r regions_to_be_parsed.bed > mpileup_from_two_bam_files.pileup

Besides, I believe your command is:

samtools mpileup -b bam_list_file -r regions_to_be_parsed.bed > mpileup_from_two_bam_files.pileup

[jing.mengrabbit]

Thanks for your advice.

Answer 1

[h.mon]

Are you sure about -r regions_to_be_parsed.bed? The help says:

-r, --region REG region in which pileup is generated

I think -r should be used as -r chr1:200-210. For using bed files as intervals, you should use -l:

-l, --positions FILE skip unlisted positions (chr pos) or regions (BED)

[jing.mengrabbit]

Thanks for your reply. I misunderstood the helper documentation. It should be -l instead of -r as you said.