简介
脚本
输入
输出
WGS
简介
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).
脚本
输入
| 任务名称 | 变量名称 | 类型 | 描述 |
|---|---|---|---|
| * WGS | split_chr | Boolean | GATK变异检测过程是否分染色体运行 |
| * WGS | snp_filter_option | String | GATK snp过滤参数 |
| * WGS | sample_name | String | 样本名称 |
| * WGS | run_fqfilter | Boolean | 是否运行fastq过滤步骤 |
| * WGS | ref_name | String | 参考序列的名称 |
| * WGS | ref | File | 参考基因组序列文件 |
| * WGS | indel_filter_option | String | GATK indel过滤参数 |
| * WGS | fqfilter_thread | Int | fastq过滤线程数 |
| * WGS | fqfilter_qualSys | Int | 输入fastq的质量体系 |
| * WGS | fqfilter_qualRate | Float | fastq过滤低质量的比例 |
| * WGS | fqfilter_outQualSys | Int | 输出fastq的质量体系 |
| * WGS | fqfilter_nRate | Float | fastq过滤N比例的阈值 |
| * WGS | fqfilter_lowQual | Int | fastq过滤低质量阈值 |
| * WGS | fqfilter_adapter2 | String | read2接头序列 |
| * WGS | fqfilter_adapter1 | String | read1接头序列 |
| * WGS | fq2 | Array[File] | 双端测序read2序列 |
| * WGS | fq1 | Array[File] | 双端测序read1序列 |
| * WGS | align_thread | Int | bwa mem比对使用的线程数 |
| * WGS | align_pu | String | bwa比对read标头RG的PU |
| * WGS | align_pl | String | bwa比对read标头RG的PL |
| * WGS | align_lib | String | bwa比对read标头RG的LIB |
| * WGS | align_id | String | bwa比对read标头RG的ID |
| * WGS | align_cn | String | bwa比对read标头RG的CN |
输出
| 任务名称 | 变量名称 | 类型 | 描述 |
|---|---|---|---|
| WGS | fqStat | File | fastq统计结果 |
| WGS | markdupBam | File | 标记去重后的bam |
| WGS | MarkdupBamBai | File | 标记去重后的bam索引 |
| WGS | gvcf | File | 变异检测产生的gvcf文件 |
| WGS | gvcfTbi | File | gvcf的索引文件 |
| WGS | vcf | File | 变异检测产生的vcf文件 |
| WGS | vcfTbi | File | vcf的索引文件 |
| WGS | filterSnp | File | 过滤后的snp |
| WGS | filterIndel | File | 过滤后的indel |
| WGS | snpStat | File | snp统计结果 |
| WGS | indelStat | File | indel统计结果 |
| WGS | snpType | File | snp类型统计结果 |
| WGS | indelLength | File | indel长度统计 |
| WGS | bamStat | File | 比对统计结果 |
| WGS | bamCumu | File | 比对累计深度分布 |
| WGS | bamHis | File | 比对深度分布 |
| WGS | bamInsert | File | 插入长度分布 |