Whole Genome Sequencing (WGS) is to sequence the species with known Genome sequence. Through sequence alignment and mutation detection, a large number of variation information can be found, including single nucleotide polymorphism (SNP), insertion deletion (INDEL).

* WGS split_chrBoolean GATK变异检测过程是否分染色体运行
* WGS snp_filter_optionString GATK snp过滤参数
* WGS sample_nameString 样本名称
* WGS run_fqfilterBoolean 是否运行fastq过滤步骤
* WGS ref_nameString 参考序列的名称
* WGS refFile 参考基因组序列文件
* WGS indel_filter_optionString GATK indel过滤参数
* WGS fqfilter_threadInt fastq过滤线程数
* WGS fqfilter_qualSysInt 输入fastq的质量体系
* WGS fqfilter_qualRateFloat fastq过滤低质量的比例
* WGS fqfilter_outQualSysInt 输出fastq的质量体系
* WGS fqfilter_nRateFloat fastq过滤N比例的阈值
* WGS fqfilter_lowQualInt fastq过滤低质量阈值
* WGS fqfilter_adapter2String read2接头序列
* WGS fqfilter_adapter1String read1接头序列
* WGS fq2Array[File] 双端测序read2序列
* WGS fq1Array[File] 双端测序read1序列
* WGS align_threadInt bwa mem比对使用的线程数
* WGS align_puString bwa比对read标头RG的PU
* WGS align_plString bwa比对read标头RG的PL
* WGS align_libString bwa比对read标头RG的LIB
* WGS align_idString bwa比对read标头RG的ID
* WGS align_cnString bwa比对read标头RG的CN
* WGS fqStatFile fastq统计结果
* WGS markdupBamFile 标记去重后的bam
* WGS MarkdupBamBaiFile 标记去重后的bam索引
* WGS gvcfFile 变异检测产生的gvcf文件
* WGS gvcfTbiFile gvcf的索引文件
* WGS vcfFile 变异检测产生的vcf文件
* WGS vcfTbiFile vcf的索引文件
* WGS filterSnpFile 过滤后的snp
* WGS filterIndelFile 过滤后的indel
* WGS snpStatFile snp统计结果
* WGS indelStatFile indel统计结果
* WGS snpTypeFile snp类型统计结果
* WGS indelLengthFile indel长度统计
* WGS bamStatFile 比对统计结果
* WGS bamCumuFile 比对累计深度分布
* WGS bamHisFile 比对深度分布
* WGS bamInsertFile 插入长度分布