PapenfussLab / gridss

GRIDSS: the Genomic Rearrangement IDentification Software Suite
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gridss results MERGE problems with other SV recognition software #672

Open HuangYihang1222 opened 3 months ago

HuangYihang1222 commented 3 months ago

Hi, I have recently been working on the identification of structural variants, using four software, Manta,delly,lumpy,gridss, I want to combine the results of these software, using SURVIVOR 1000 2 1 10 50, but there are a lot of GT information like ./. in the results. In these software, only the results of gridss have no genotype information. Would you like to answer if there is any better solution? Thank you!

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HuangYihang1222 commented 3 months ago

Correct:SURVIVOR 1000 2 1 1 0 50 for individual results merged from 4 softwares, SURVIVOR 1000 1 1 1 0 50 for population results merged from individuals merged above.

HuangYihang1222 commented 1 month ago

你好,我目前也在做这个工作,想问一下你进行的顺利吗? 可以一起交流一下吗?

你好,我将GRIDSS的VCF文件自己写脚本更改了一下格式之后,用SVTyper进行了基因分型,随后用SURVIVOR进行merge,似乎这里的./.代表的是这个个体没有这个SV的意思,我将它视为0/0。不知道您是怎么处理不同软件的群体SV识别以及合并的呢?

SunWinner01 commented 1 month ago

hi,想问一下,你使用svtyper进行分型得到结果吗?不知道为什么,我用svtyper进行分型gridss的vcf文件,报错啦,并且没有生成想要的结果文件内容。(一打开里面什么都没有) @HuangYihang1222