Samtools: extract multiple cromosomes/scaffolds from bam file

[Anti]

Hi,
I want to create a bam file containing three or four chromosomes/scaffolds.
I only know this command

samtools view -b align.sort.bam Chr06 > chr06.bam

[dpryan]

You can just use samtools merge with process substitution:

samtools merge merged.bam <(samtools view -b foo.bam chr1) <(samtools view -b foo.bam chr2) ...

A likely faster method might be to just make a BED file containing those chromosomes/contigs and then just:

samtools view -b -L chromosomes.bed foo.bam > subset.bam

[Anti]

Thanks so much, dpryan! but this command don't create a bam from two cromosomes.

i used this :

samtools merge merged.bam <(samtools view -b SE.bam chr1) & (samtools view -b SE.bam chr2)

using your suggestion and works!

[dpryan]

Adding a random "&" into a command will tend to break things.

[Anti]

You are right.
Command works but show this:
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] EOF marker is absent. The input is probably truncated.


But the output bam is correct.

Thanks so much, dpryan.