Samtools sorted file question

[lre1234]

Hi all,
I did a sam to bam file conversion and the resulting bam file was 5.0GB in size. I then did a samtools sort on the bam file and the resulting sorted bam file is now 3.7GB in size. Is this size decrease in the unsorted vs. sorted bam files normal and expected or is information being lost.

I also did a samtools flagstat on both files and they both showed the same number of reads.

I'm just curious that I am not loosing anything in my sorting bam, but not sure what can be lost in that step.

Thanks

[maubp]

Yes, this normal (and has been asked and answered on this forum before - did you have trouble with the search tool?).

By sorting the BAM file by mapping position, similar sequences are placed next to each other, which compresses better. Therefore while the raw uncompressed data is the same size, the GZIP/BGZF compression used in BAM can shrink things more than the unsorted BAM file.