Tassel gbs pipeline: MergeDuplicateSNP_vcf_Plugin question

[balsampoplar]

I am using the tbt2vcfPlugin and the MergeDuplicateSNP_vcf_Plugin from Tassel version 3.0. The user manual talks only about the hapmap version of the second plugin which includes flags such as -callHets and -misMat. However, these flags seem to be missing from the vcf version of this plugin.

Is a workaround available? Could these flags be applied at a different stage of the pipeline?

Thanks

[balsampoplar]

Answering my own question here. These flags are not implemented in the vcf version of this plugin because the depth information is retained in vcf format. Thus these flags are unnecessary.