1.1. WES#
1.1.1. QC#
1.1.1.1. fastp#
fastp is a tool designed to provide ultrafast all-in-one preprocessing and quality control for FastQ data.
1.1.1.2. Conpair#
Conpair is a fast and robust method dedicated for human tumor-normal studies to perform concordance verification (i.e. samples coming from the same individual), as well as cross-individual contamination level estimation in whole-genome and whole-exome sequencing experiments.
Note
1.1.2. Reads mapping and PCR deduplication#
Clindet use BWA to mapping short reads to genome,GATK was use to mark PCR duplicate reads for downstream analysis.
1.1.3. Reads mapping statistics#
GATK was used to calculate the reads mapping percentage and coverage of each mapping BAM file.
1.1.4. GATK preprocess#
Firstly,read mapping quality was [def]: nv:sphinx:std#inde