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
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!