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Old 04-09-2010, 04:16 AM   #1
bair
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Default ELAND format to SAM

Hello all,

I have alignments in Eland format, how can I use samtools for SNPs calling?

Thanks
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Old 04-09-2010, 04:57 AM   #2
kmcarr
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There is no single "Eland" format. The Eland aligner outputs in a number of different (albeit very similar) formats. The most commonly used is an export file. If you have a file in the export format then you can simply convert it using the export2sam.pl script which is included in the samtools package.
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Old 04-09-2010, 05:07 AM   #3
bair
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Quote:
Originally Posted by kmcarr View Post
There is no single "Eland" format. The Eland aligner outputs in a number of different (albeit very similar) formats. The most commonly used is an export file. If you have a file in the export format then you can simply convert it using the export2sam.pl script which is included in the samtools package.
export2sam.pl is what I need.

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