Question: simulating variants with specific frequency using GATK
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gravatar for christacaggiano
2.4 years ago by
UCSF
christacaggiano30 wrote:

Hi,

Given a VCF file that I want to use GATK SimulateReadsForVariants to generate simulated data containing those variants (mostly indels) is there a way to specify that the variants be generated at a specific allele frequency?

This is the package I hope to use: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_simulatereads_SimulateReadsForVariants.php

I am testing the sensitivity of various indel calling algorithms and want to see how these algorithms perform when the variants are at 10%, 5%, 1% etc. It is okay if it is a naive method of simulating the data at this point, because we are only in the first steps of this study, but I would also appreciate advice on more advanced techniques if you have any :)

Thanks!

gatk vcf • 735 views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 2.4 years ago by christacaggiano30
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