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Old 03-25-2013, 01:40 PM   #1
rahul
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Default Samtools sort vs Picard Sortsam

Hi all,

Which is a better pick for sorting large SAM files in terms of memory requirement and run time: sortSam from Picard or Samtools sort function. Could you please direct me to the thread if it is already discussed and i missed it.

Thank you,

Rahul
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Old 02-10-2015, 11:39 PM   #2
ymc
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I want to know SortSam vs samtools sort, too.

I think MarkDuplicates is better than rmdup because the former can handle duplicates across break points.
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Old 02-11-2015, 12:06 AM   #3
sklages
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Why don't you just try?
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Old 02-11-2015, 12:58 AM   #4
ymc
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Quote:
Originally Posted by sklages View Post
Why don't you just try?
Because they give the same results after I try. I think there might be differences in edge cases, for example, when it is piped from bwa-mem. But I don't know what the edge cases are.
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Old 02-11-2015, 01:30 AM   #5
sklages
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So if you get the same results in terms of mem and runtime for huge files, just decide for the one you're more familiar with. Edge cases are usually very specific, so if you don't encounter any problems with your regular files, no need to worry :-)
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Old 02-11-2015, 12:04 PM   #6
swbarnes2
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I think Picard's sortSam puts a line in the header indicating that the file is sorted, which samtools does not. But for lots of applications this doesn't matter.
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Old 02-11-2015, 01:12 PM   #7
dpryan
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Quote:
Originally Posted by swbarnes2 View Post
I think Picard's sortSam puts a line in the header indicating that the file is sorted, which samtools does not. But for lots of applications this doesn't matter.
Are you sure about that? The header is grabbed from the first tmp file written.
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