samtools sorting outfile is not as large as input file
 

I tried to sort a bam file for paired-end genomic data using samtools sort option. BAM file size is about 85gb. I sorted them on read names instead of chromosome coordinates. The output file is about 79gb. I am wondering where did 6gb of data from the input file go? Has anyone seen this type of inconsistency before?

Thanks.

That's the magic of sorting a .bam; it comes out smaller, because it compresses better.

If you do flagstat on the .bam before and after sorting, you'll see that they have the same number of reads.

Definitely makes sure you have the right number of reads and that the sort did not prematurely terminate.

Thanks a lot......... how would I know if the sorted file is complete?

samtools flagstat or use samtools view -c to the count the reads