Introduction
Script
Input
Output
WGS
Introduction
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).
Script
Input
| Task name | Attribute name | Type | Description |
|---|---|---|---|
| * WGS | split_chr | Boolean | GATK variant calling by chromosome |
| * WGS | snp_filter_option | String | option of GATK snp filter |
| * WGS | sample_name | String | sample name |
| * WGS | run_fqfilter | Boolean | run fastq filter or not |
| * WGS | ref_name | String | reference name |
| * WGS | ref | File | reference sequence file |
| * WGS | indel_filter_option | String | option of GATK indel filter |
| * WGS | fqfilter_thread | Int | threads number used in fastq filter |
| * WGS | fqfilter_qualSys | Int | input fastq quality system |
| * WGS | fqfilter_qualRate | Float | low quality rate in fastq filter |
| * WGS | fqfilter_outQualSys | Int | output fastq quality system |
| * WGS | fqfilter_nRate | Float | N rate threshold in fastq filter |
| * WGS | fqfilter_lowQual | Int | low quality threshold in fastq filter |
| * WGS | fqfilter_adapter2 | String | adapter sequence of read2 |
| * WGS | fqfilter_adapter1 | String | adapter sequence of read1 |
| * WGS | fq2 | Array[File] | paired-end sequenceing read2 |
| * WGS | fq1 | Array[File] | paired-end sequenceing read1 |
| * WGS | align_thread | Int | number threads used in bwa mem |
| * WGS | align_pu | String | PU in bwa RG |
| * WGS | align_pl | String | PL in bwa RG |
| * WGS | align_lib | String | LIB in bwa RG |
| * WGS | align_id | String | ID in bwa RG |
| * WGS | align_cn | String | CN in bwa RG |
Output
| Task name | Attribute name | Type | Description |
|---|---|---|---|
| WGS | fqStat | File | output fastq statistical results |
| WGS | markdupBam | File | output bam which duplicate reads was tags or remove |
| WGS | MarkdupBamBai | File | index of markdup bam |
| WGS | gvcf | File | gvcf file of variant calling |
| WGS | gvcfTbi | File | gvcf index file |
| WGS | vcf | File | vcf file of variant calling |
| WGS | vcfTbi | File | vcf index file |
| WGS | filterSnp | File | filter snp |
| WGS | filterIndel | File | filter indel |
| WGS | snpStat | File | snp statistical results |
| WGS | indelStat | File | indel statistical results |
| WGS | snpType | File | snp type statistical |
| WGS | indelLength | File | indel length statistical |
| WGS | bamStat | File | output bam statistical |
| WGS | bamCumu | File | align cumulative depth distribution |
| WGS | bamHis | File | align depth distribution |
| WGS | bamInsert | File | insertion length distribution |