GATK Hard-filter 过滤变异结果推荐阈值
GATK Hard-filter 过滤变异结果推荐阈值
Hard-filter阈值探究
GATK4官网给出的推荐阈值：For SNPs:
QD < 2.0
MQ < 40.0
FS > 60.0
SOR > 3.0
MQRankSum < -12.5
ReadPosRankSum < -8.0
For indels:
QD < 2.0
ReadPosRankSum < -20.0
InbreedingCoeff < -0.8
FS > 200.0
SOR > 10.0
查看GATK4原始网页：https://software.broadinstitute.org/gatk/documentation/article?id=11097该阈值选择来自于GATK4官网的推荐，阈值依据于比较真 vs. 假 snp的特征值（annotation values）统计分布
One of the most helpful ways to approach hard-filtering is to visualize the distribution of annotation values for a truth set called using a particular pipeline. These distributions are sharped by both the pipeline methodology and the underlying physical properties of the sequence data; so for a given pairing of data generation technology + analysis pipeline, you can derive filtering thresholds based on what the distributions look like for the truth set
评估数据来源：1000Genomes 中的 whole genome trio
- 发表于 2020-06-25 09:38
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- 分类：重测序
