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Old 01-25-2010, 01:44 AM   #1
bair
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Default Compare SNPs

Hello, does someone know how to comare two SNP calling files in gff format?

Thanks for your help!
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Old 01-25-2010, 05:35 AM   #2
quinlana
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I would suggest Galaxy if you want a web interface or BEDTools if you prefer command line tools.

Aaron
Disclosure: I am the author of BEDTools.
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Old 01-25-2010, 06:32 AM   #3
bair
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That's exactly what I am looking, very useful.

Thanks
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Old 01-25-2010, 09:18 AM   #4
bair
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installed BEDtools (BEDTools.v2.4.2.tar.gz), but only has bamToBed under bin/

other tools?
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Old 01-25-2010, 11:40 AM   #5
quinlana
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That's quite odd.

Did you type "make" then Enter in the BEDTools directory? This should have compiled all 17 tools and placed the resulting binaries in bin/
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Old 01-27-2010, 02:38 AM   #6
bair
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Hi Quinlana,

Got all 17 tools with the help from our admin. BTW, when I only type bedtools, all the 17 tools should be list, otherwise I have to go to the path to find out which function bedtools has.

Thanks
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