Comments (7)
另外,下面这一步重新mapping 20个个体的步骤不是很理解,并且一共有31个个体,为什么只选择了20个个体重新mapping?
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之前caller里对SVs的定义不一样,有些是把长度大于30bp的也当做SV了,但是我们的定义是50bp。所以clean SVs这步是把长度低于50bp的变异去掉。
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另外,下面这一步重新mapping 20个个体的步骤不是很理解,并且一共有31个个体,为什么只选择了20个个体重新mapping?
这步vg流程使用的用来去除重复SVs的。相同的SV不同的软件去做,检测的不完全一致。这里的20个样本,不是三代,是20个多样性丰富的高深度的二代个体。需要注意的是,这步有可能去除多等位的SVs。
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谢谢您的回复,明白了
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另外,WGS --model vcf --type mergeSVs 这个mergeSV的操作的具体功能是什么呢? 我使用这个命令原本有8W个SV 后面merge一下变成了7W,不知道这一步为什么会减少SV的数量。
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这步是根据vg软件要求准备的输入,是否需要merge看你们的实际情况。merge的时候,若ref或者alt的碱基中有N,则会被过滤掉。因为这些都个性化处理,所以我们没有对每个参数进行详细说明,每个参数的功能,可参考WGS源码。
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好的 谢谢您
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