About samtools sort

[Richard.Y]

I have sorted the .bam files with samtools sort, but then it still said that [bam_pileup_core] the input is not sorted (chromosomes out of order) when I running samtools mpileup

[Heisman]

Could you post the exact commands you ran (to generate the original bam file, sort, and then to run pileup? Also maybe do samtools view on the sorted bam file and look to see that it is indeed sorted by coordinates.