gridss results MERGE problems with other SV recognition software

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GRIDSS: the Genomic Rearrangement IDentification Software Suite

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gridss results MERGE problems with other SV recognition software #672

Open HuangYihang1222 opened 2 months ago

HuangYihang1222 commented 2 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!

HuangYihang1222 commented 2 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 4 weeks 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 3 weeks 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