Inquiry on Using Pooled Samples for Population History Inference with SMC++

[JcWukkkk]

Dear authors,

I hope this email finds you well. My name is Chuan Jiang, and I am a researcher in the field of ornithology and genetics. I am currently working on a project involving population history inference for a particular avian species.

I am writing to inquire about the feasibility of using pooled samples (multiple individuals mixed for next-generation sequencing) for demographic history inference with SMC++. Specifically, I would like to know if it is possible to use such pooled data for analysis with SMC++.

Additionally, after aligning the pooled data to a reference genome and obtaining BAM files, I am seeking recommendations on the best methods to generate VCF files suitable for SMC++ analysis. Are there any particular tools or pipelines you would recommend for this purpose?

Thank you very much for your time and assistance. I look forward to your response.

Best regards,

Chuan Jiang