yaozhou89 / tgg Goto Github PK

In your method, Genotypes of Structural variants (SVs) in 706 accessions with following code:

multigrmpy.py -i /public10/home/sci0011/projects/tomato2/08_paragraph/02_vcf/SV.paragraph.vcf -m /public10/home/sci0011/projects/tomato2/08_paragraph/01_bam/samples_${sample}.txt -r ~/data/ref/SL5.0/SL5.0_chr_number.fa -o . --threads 64

but how to gain the file "SV.paragraph.vcf" ?

Hi, the 1.Genome_asembly/1.contig part reports that

Flye, Hicanu and Hifiasm are used to assemble primary genome. GALA is used to fillter the potential miss-assembly regions. WGS is manual software intergrated in pipeline.

but I am not able to find all the code/scripts about it. For example, I see that a script called draft_comp.sh is missing, I don't see where flye, canu, gala are called, etc...

I state that I am a newbie with snakemake, and I apologize if this is the problem.

Hello, Mr. Zhou!
I had a question when I read your code about dedup merged SV. Is this step necessary? Does it mean that if I do long-reads sequencing (HiFi or ONT) on some individuals, I also need to do short-reads sequencing (>20x) on them? This ensures that I can use their short reads for redup after merging SVs?

您好，我在您公布的TGG1.1 vcf数据集中看到所有的变异位点都被merge成一个样本名（图一）,但是我看到有些构建vg图是包含所有的样本信息在vcf文件里面的，我想咨询下您，这两种方法有什么区别呢？为什么把多个样本的变异全部集中在一个样本集合内呢？
图1：TGG1.1 vcf

图2：human vg vcf文件

Yaozhou89，您好，在《Graph pangenome captures missing heritability and empowers tomato breeding》这篇文章的reference的5.1中提到了您使用simug进行simulated genome以及使用 art_illumina 进行 simulated short reads 的相关工作，但是我在 Benchmark study of graph simulation 部分并没有找到更加详细的介绍，simug 部分的shell也是空的，我想知道您是否能够更新补充这一部分内容。

此外，在 http://solomics.agis.org.cn/tomato/ftp 数据库中也没有找到simulation相关的short reds数据，不知道您是否有将相关数据传入其他数据库，或者您是否能够提供相关数据。

感谢您的宝贵时间与帮助。

Hi,Zhou!
I read your article on the tomato pan-genome, fantastic job! But I get confused when I read your method section about genome-wide association study, you said that "After pruning using PLINK (v.2.0) with the parameter ‘-indep-pairwise’ set to ‘50 5 0.2’, the pruned SNPs were used for the kinship matrix (genetic relationship matrix; GRM). For SNPs and indels, the pruned dataset (-indep-pairwise 100, 1, 0.98) was used". Does this sentence mean that the second parameter is used when the sum of snp and indel is in the vcf file? I see that your article also includes other types, sv and indel separately, or SNP+indel+SV, does this need to filter the LD, what parameters do you use?
Sorry to bother u. Thanks a million!

In your pipeline, the heritability assessment with a single variant set was provided， but I want to analyze categories of genetic variants jointly following your article, can you provide me with a more detailed code? thanks~

Dear Teacher Zhou:
Recently, I selected the SL5.0 tomato genome in Graph pangenome captures missing heritability and empowers tomato breeding as a reference genome. I would like to know the centromere position of each chromosome of SL5.0 in Figure 1a. Thank you!
Very much looking forward to your reply !

Hi, there are multiple missing images in the markdown files. The links are broken as they point to a local folder. Here are a few of them:

in https://github.com/YaoZhou89/TGG/blob/main/1.Genome_assembly/1.contig/Readme.md

in https://github.com/YaoZhou89/TGG/blob/main/1.Genome_assembly/2.scaffold/Readme.md

in https://github.com/YaoZhou89/TGG/blob/main/2.Genome_annotation/Readme.md

in https://github.com/YaoZhou89/TGG/blob/main/4.Graph_pangenome/1.construction_graph_genome/Readme.md

尊敬的周老师@YaoZhou89
请问在如下步骤中，多个个体以什么方式合并到一个vcf中，多个样本合并还是融合到一个样本？

这里的cleanSV行使了什么功能？

另外，在如下步骤中，如果我的流程中不涉及使用多个SV calling软件，只用了一个软件，我可以不使用这个步骤来对SV去重吗？

敬上
强森

Dear Dr. Zhou,

Thanks a lot for this fantastic work!
I wonder how did you quantify structural variations when constructing a GRM for SVs.

Many thanks!

Sincerely,
Stella.

In your pipeline, The prepare_gene_expression.R script is missing in 5.Genetic_analysis, can you provide this code? Thanks~