Extracting a chromosome from an indexed bam file?

Question

[tuj92050]

This is for a course I am currently taking. I have downloaded an indexed bam file (.bai) of all the exome reads from thr 1000 genomes project. The next step in this assignment is extracting the reads for chromosome 22 of this file. I tried samtools to do this

samtools view -b NA20515.bam.bai chr22 > chr22.bam

But I am met with the error

[E::hts_hopen] Failed to open file NA20515.bam.bai
[E::hts_open_format] Failed to open file NA20515.bam.bai
samtools view: failed to open "NA20515.bam.bai" for reading: Exec format error

Obviously I don't think I can do this with samtools. Is there any other way to do this?

[GenoMax]

You should do samtools view on bam file, not .bai file.

[Pierre Lindenbaum]

you want

samtools view -b NA20515.bam chr22 > chr22.bam

not the bai file

[tuj92050]

I just tried that and I got the error "random alignment retrieval only works for indexed BAM or CRAM files"

[swbarnes2]

It's not clear to me; do you have both NA20515.bam and NA20515.bam.bai? Are they together in the same directory?