April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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154
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第
5
章
现在我们若想结合使用多个过滤器，又该如何操作？我们可以完善
QD
过滤器的过
滤效果，争取过滤掉
DP
值极高的变异识别结果，因为这些结果大都属于假正类。
我们再次在先前输出结果上，运行
VariantFiltration
工具，只不过这次用新过滤器。
我们亦可使用原始数据，同时用两个过滤器，如下所示：
# gatk VariantFiltration \
-R ref/ref.fasta \
-V vcfs/motherSNP.vcf.gz \
--filter-expression "QD < 2.0 || DP > 100.0" \
--filter-name "lowQD_highDP" \
-O sandbox/motherSNP.QD2.DP100.vcf.gz
过滤表达式中的双管道符（
||
）等价于逻辑或（
OR
）表达式。其使用次数不限，并
且你还可以用
&&
表示逻辑与（
AND
）运算符，但是在构造极其复杂的过滤语句中
要当心。有时最好保持过滤语句简单，并将其拆分为单独组件，这样既简洁又方便
测试。
GATK
硬过滤工具为调试这些命令提供多种选项，其中包括对缺失值的处理方式。
可是你要记住，硬过滤是一种相对简单的过滤机制，它算不上
GATK
最佳实践。该
方法的优势在于，如果你能很好地理解注释的含义及其计算方式，它则非常直观。
实际上，它在专家级分析师手里可以做到非常有效。但是需调试的地方非常多，初
学者难以胜任，并且对于每个新项目往往需要新的分析工作，因为适用于一个数据
集的过滤阈值往往不能直接应用于其他数据集。 ...
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.