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!
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jing.mengrabbit •
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)
Thanks for your reply. I misunderstood the helper documentation. It should be -l instead of -r as you said.
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Hello jing.mengrabbit,
Please use the formatting bar (especially the
codeoption) to present your post better.For example:
Besides, I believe your command is:
Thanks for your advice.