Question

What Is The Difference Between 'Samtools Index' And 'Buildbamindex' From Picard Tools

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11.2 years ago

cpcantalapiedra ▴ 170

What is the difference between both tools and between the indexed generated? Does matter which one I choose?

picard samtools ngs mapping • 3.8k views

ADD COMMENT • link updated 4.4 years ago by ilykos ▴ 10 • written 11.2 years ago by cpcantalapiedra ▴ 170

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Any ideas about which one is faster?

ADD REPLY • link 4.4 years ago by ilykos ▴ 10

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samtools index you can specify more than one thread with -@ option.

ADD REPLY • link 4.4 years ago by GenoMax 147k

score 5 · Answer 1 · 2013-09-25

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11.2 years ago

Devon Ryan 104k

They do the same thing, you can use either one.

ADD COMMENT • link 11.2 years ago by Devon Ryan 104k

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For the OP: Both tools implement the algorithm described in the SAM specification: http://samtools.sourceforge.net/SAMv1.pdf

ADD REPLY • link 11.2 years ago by Dan D 7.4k