Getting 'Samtools View' To Work On Multiple Bamfiles Simultaneously

Question

[Kwame]

Hello,

I want to extract regions of multiple bamfiles kept as seperate files using the following samtools command:

samtools view -b a.bam refsequence :113111720-113112765 > aoutput.bam

How can I modify the above command so it works on multiple bamfiles example:a.bam b.bam c.bam d.bam simultaneously? I am currently doing this one bamfile at a time and it is taking forever. Thanks

Answer 1

[lh3]

To output one BAM:

samtools merge -r chr1:100-1000 - *.bam > out.bam

To output multiple BAMs:

ls *.bam|sed s,.bam,,|xargs -i echo samtools view -b {}.bam chr1:100-1000 > part-{}.bam|sh

[Marvin]

Or far less complicated:

for f in *.bam ; do samtools view -b $f chr1:100-1000 > part-$f ; done

Answer 2

[Swbarnes2]

I don't think you can. If you made the .bam files with read group information, you could merge them togehter, then run the view command on that.