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Old 07-18-2013, 04:48 AM   #1
mmmm
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Hello everyone,
I was wondering how do you manage to get "consensus sequence" from the mapped BAM file?
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Old 07-18-2013, 05:09 AM   #2
GenoMax
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http://chipster.csc.fi/manual/samtools-consensus.html
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Old 07-18-2013, 05:17 AM   #3
krobison
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If anybody assembles a SEQAnswers bioinformatics FAQ, this should probably be #1
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Old 07-18-2013, 05:27 AM   #4
mmmm
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Quote:
Originally Posted by GenoMax View Post
Many thanks for this
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Old 07-18-2013, 07:28 AM   #5
Heisman
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One point I'll add; samtools mpileup by default discards reads marked as duplicates. If you want to retain those, see this thread: http://seqanswers.com/forums/showthread.php?t=22752
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