a framework for DNA seq mapping and call structural variant for WGS data.
Recently WGS processing standards were proposed by Regier A. et al. 2017 Nature Comm. Here this pipeline includes these guiding principles for future integrateion of different WGS bam file from different source of public database, likes TOPMed. SV call was made by smoove Most tools are already satisfied at ACCRE(under CQS group at VUMC), except thess two need to be installed
```
Program: sv_pipeline
Version: 0.1
Author: Youhuang Bai ([email protected])
usage: sv_pipeline <command> [options]
command: mapping align FASTQ files with BWA-MEM, add MC MQ Tags with samblaster and sort by name
refine apply gatk recalibration to it
call SV call with lumpy in smoove
merge merge SVs with smoove
genotype genotype SVs with svtyper in smoove
combine combine all samples into one file
annotate annotate with genome annotation
```
git clone https://github.com/biobai/sv_pipeline.git
cd sv_pipeline
chmod a+x bin/sv_pipeline
mapping test fastq file to hg19(default)/hg38 genome
```
sv_pipeline mapping -o test ./test.R1.fq.gz ./test.R2.fq.gz
```
refine the bam file
```
sv_pipeline refine -o test -O ./ -V hg38 -i test.bam
```
smoove call
```
sv_pipeline call -i ./test.mkDup.sorted.recal.bam -o test -V hg38
```
smoove merge
```
sv_pipeline merge -o test -O ./ -i *.genotyped.vcf.gz -V hg38
```
smoove genotype
```
sv_pipeline genotype -v test.sites.vcf.gz -i ../2_bamMerge_hg38/result/SL345196/SL345196.mkDup.sorted.recal.bam -o SL345196 -O ./ -V hg38
```