Filter hapmap by sites

PTyagi

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Oct 16, 2015, 1:19:29 PM10/16/15

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Hello,

I am using Tassel 5 for calling SNPs on my data. Apart from minor allele frequency and missing data, I would also like to filter sites based on heterozygosity. I am using site summary to find sites with acceptable level of proportion heterozygosity in order to filter hapmap file for highly heterozygous sites. Is there a way to filter the raw hapmap file using this selected set of sites in command line. Tassel GUI allows filtering based on sites names but it is not feasible to select thousands of SNPs manually. I would really appreciate if someone could offer any suggestions.

Thanks

Priyanka

Terry Casstevens

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Oct 16, 2015, 1:24:04 PM10/16/15

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-includeSiteNames
-includeSiteNamesInFile
-excludeSiteNames
-excludeSiteNamesInFile

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/Tassel5PipelineCLI.pdf

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PTyagi

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Oct 16, 2015, 1:43:07 PM10/16/15

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Thanks Terry

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