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Old 04-15-2011, 01:56 AM   #1
Sylphide
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Default Samtools sort output smaller than input

Hello,
I have a problem with samtools sort : my output files are smaller than my input files when they should be identical since only the lines order is changed !
Does anyone know this problem and a solution ?
thanks
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Old 04-15-2011, 03:06 AM   #2
jkbonfield
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It is correct and is caused by higher compression ratios from zlib when data is sorted.
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Old 04-15-2011, 09:10 AM   #3
swbarnes2
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Right, this is normal. You can confirm that yourself by running flagstat on the unsorted and sorted file. They will have the same number of reads.
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Old 04-15-2011, 02:12 PM   #4
Sylphide
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Indeed they have the same read number.
Many thanks for your help !
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