STACKS should be fine.
At the GBS Workshop I attended at Cornell (with speakers including Dr. Buckler), we were told that any tool you can use to analyze RAD data, you can also use to analyze GBS data. So there should be no problem using STACKS for your GBS data.
Also, last I checked bwa and bowtie2 were the aligners mentioned in GBS training by the Buckler group.
disclaimer: I have no experience with STACKS. As part of the Maize Diversity Project, which Ed Buckler heads, I use the Buckler GBS pipeline to work with GBS/RAD maize data.
At the GBS Workshop I attended at Cornell (with speakers including Dr. Buckler), we were told that any tool you can use to analyze RAD data, you can also use to analyze GBS data. So there should be no problem using STACKS for your GBS data.
Also, last I checked bwa and bowtie2 were the aligners mentioned in GBS training by the Buckler group.
disclaimer: I have no experience with STACKS. As part of the Maize Diversity Project, which Ed Buckler heads, I use the Buckler GBS pipeline to work with GBS/RAD maize data.
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