Extract single chromosome reads from Bam file

Question

[marco.barr]

I'm trying to extract the reads relating to chrM from an aligned BAM file but without success. These are my commands:

samtools view -h Linfo_mt6394_aligned_sorted.bam chrM > Linfo_mt6394_chrM_aligned.sorted.sam 
samtools view -bS Linfo_mt6394_chrM_aligned.sorted.sam > Linfo_mt6394_chrM_aligned.sorted.bam

when I check with samtools idxstats results all chromosome. Why? Are there alternative ways to extract single chromosome reads from a BAM file?

Thanks

Answer 1

[ATpoint]

You see that all chromosomes are still in the header, but only chrM will have reads. The header is not updated. Note that the sam/bam conversion is unnecessary.

samtools view -h -o Linfo_mt6394_chrM_aligned.sorted.bam Linfo_mt6394_aligned_sorted.bam chrM 

That command is the same without unnecessary conversion.