gatk过滤_GATK Hard-filter 过滤变异结果推荐阈值

最新推荐文章于 2024-07-29 13:46:30 发布

曾伴浮云归晚翠

最新推荐文章于 2024-07-29 13:46:30 发布

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Hard-filter阈值探究

GATK4官网给出的推荐阈值：For SNPs:

FS > 60.0

SOR > 3.0

MQRankSum

ReadPosRankSum

For indels:

ReadPosRankSum

InbreedingCoeff

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