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Old 06-20-2011, 01:54 PM   #1
andy11
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Default Heterozygosity with short read simulators?

I was wondering if short read simulators like wgsim (from samtools) create heterozygosity from the input fasta file and if so, what they do to create it.

Thanks for any help
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Old 06-20-2011, 06:54 PM   #2
nilshomer
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Yes, they store two copies of the reference, and when they mutate it (for SNPs/indels), some fraction mutates only one copy. See the source code for details.
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