Question about data

[Anuradha]

I want to understand the data hosted in this repo.

1. Giessen_dataset folder has two files.
   • Is the cip_ctx_ctz_gen_pheno.csv file contain labels for resitance? 1=resistant and 0=susceptible?
   • Is the cip_ctx_ctz_gen_multi_data.csv file contain the transformed SNPs? A,C,G,T,N represented as 1,2,3,4,0?
2. Is there a way to reproduce the CGR representation? Or have I missed something?

Really appreciate your support on this.

Thanks
A

[Anuradha]

Could you also make a comment on INDELs, there is some processing in 01_SNPs_calling.sh but not sure from paper how they were handled.

Also how did you treat multi-allelic variants? I see you are using -m flag in bcftools.

[SHIP]

我想了解此存储库中托管的数据。

1. Giessen_dataset文件夹有两个文件。
   • 文件是否包含恢复标签？ 和？cip_ctx_ctz_gen_pheno.csv``1=resistant``0=susceptible
   • 文件是否包含转换后的 SNP？ 表示为 ？cip_ctx_ctz_gen_multi_data.csv``A,C,G,T,N``1,2,3,4,0
2. 有没有办法重现 CGR 表示？还是我错过了什么？

非常感谢您对此的支持。

谢谢 A

Hello, could you let me know if you've successfully replicated FCGR? If so, could you please guide me through it? Thank you very much.