Single population genotype simulation

[MatusBuci]

Hey all,

I would like to use G2P software for my population genetics analysis. I converted the dbSNP VCF file into a ped and map file but when I start a single population simulation I get no results. When I compared my ped and map data with the example dataset provided by the author of this software I found out that my chromosomes are in different coding. I can't convert chromosome codes into numerical coding e.g. 1-23 because the reference genome of my species doesn't include chromosome names only GenBank seq accessions (e.g. KZ293970.1. I am assuming that a different map file format is causing some error during genotype simulation. Can you give me some advice on how to process my data in order to start genotype simulation or if it is even possible to simulate genotypes with such data. In the attachment I send you the first rows of my map file so you can see the difference. Thanks.

Stacks v2.53; PLINK v1.07; December 24, 2020

KZ293964.1 1_74 0 60584
KZ293964.1 19_241 0 157297
KZ293964.1 19_83 0 157455
KZ293964.1 34_117 0 316668
KZ293964.1 47_342 0 510213
KZ293964.1 58_92 0 568098
KZ293964.1 58_302 0 568308
KZ293964.1 93_10 0 913819
KZ293964.1 93_45 0 913854
KZ293964.1 148_223 0 1412914
KZ293964.1 148_120 0 1413017

[XiaoleiLiuBio]

Hi there, Thank you for using G2P. We will check the problem you raised. BTW, we have moved the simulation functions to our newly developed package SIMER （https://github.com/xiaolei-lab/SIMER). Could you please try it?

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----------原邮件信息---------- 发件人："Matus Buci" ***@***.***> 收件人："XiaoleiLiuBio/G2P" ***@***.***> 抄送人："Subscribed" ***@***.***> 主题：[XiaoleiLiuBio/G2P] Single population genotype simulation (Issue #8) 发送时间：2024-02-12 19:43:29 Hey all, I would like to use G2P software for my population genetics analysis. I converted the dbSNP VCF file into a ped and map file but when I start a single population simulation I get no results. When I compared my ped and map data with the example dataset provided by the author of this software I found out that my chromosomes are in different coding. I can't convert chromosome codes into numerical coding e.g. 1-23 because the reference genome of my species doesn't include chromosome names only GenBank seq accessions (e.g. KZ293970.1. I am assuming that a different map file format is causing some error during genotype simulation. Can you give me some advice on how to process my data in order to start genotype simulation or if it is even possible to simulate genotypes with such data. In the attachment I send you the first rows of my map file so you can see the difference. Thanks. # Stacks v2.53; PLINK v1.07; December 24, 2020 KZ293964.1 1_74 0 60584 KZ293964.1 19_241 0 157297 KZ293964.1 19_83 0 157455 KZ293964.1 34_117 0 316668 KZ293964.1 47_342 0 510213 KZ293964.1 58_92 0 568098 KZ293964.1 58_302 0 568308 KZ293964.1 93_10 0 913819 KZ293964.1 93_45 0 913854 KZ293964.1 148_223 0 1412914 KZ293964.1 148_120 0 1413017

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