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Old 07-12-2013, 02:46 AM   #1
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Default Consensus sequence out of BAM+VCF with low coverage areas masked?


I'm wondering if it's possible to create a consensus sequence that combines the data of BAM/SAM files and filtered VCF files so that areas of low coverage could also be masked? My intention is to do a sliding window analysis of some population genetic parameteres (Nei's pi, Watterson's theta etc.). Something like GATK FastaAlternateReferenceMaker looks promising, but the problem is that areas of low coverage (<7) must be absent from the consensus.
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consensus sequence, coverage, population genetics, sliding, window

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