前言
本文介绍了两种体细胞变异检测pipeline:
- TNscope:使用Sentieon特有的算法,拥有更快的计算速度和更高的计算精度,对临床基因诊断样本尤其适用;
- TNhaplotyper2:匹配Mutect2(现在匹配到4.1.9)结果的同时,计算速度提升10倍以上。
关于TNscope和TNhaplotyper2的完整脚本,可访问:https://github.com/Sentieon/sentieon-scripts/tree/master/example_pipelines/somatic
Sentieon软件下载地址:https://www.insvast.com/sentieon
TNscope pipeline的数据处理流程,主要针对WES和Panel (200-500x depth, AF > 1%)
第一步:Alignment
# ******************************************
# 1a. Mapping reads with BWA-MEM, sorting for tumor sample
# ******************************************
( sentieon bwa mem -M -R "@RG\tID:$tumor\tSM:$tumor\tPL:$platform" \
-t $nt -K 10000000 $fasta $tumor_fastq_1 $tumor_fastq_2 || \
echo -n 'error' ) | \