Pipeline-of-genomics

This workshop records the whole processing steps of genomics analysis in CC-LY Lab, including alignment, quality control, somatic and germline SNV detected and CNV detected from fasta files. There were two individual pipelines designed for executing on mouse and human data, respectively. Here, we referred the GATK workshop for SNV calling, CNVkit workshop for CNV detecting.

• The software we need:

#bwa
Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188

#gatk4.1
GATK=/mnt/data/user_data/xiangyu/programme/gatk-4.1.3.0/gatk

#cnvkit
cnvkit.py version
0.9.9

#vep
/mnt/data/userdata/xiangyu/programme/vcf2maf-master/vcf2maf.pl

#Rscript
Rscript --version
R scripting front-end version 3.5.1 (2018-07-02)

#perl
perl --version
This is perl 5, version 22, subversion 1 (v5.22.1) built for x86_64-linux-gnu-thread-multi
(with 77 registered patches, see perl -V for more detail)

#The extend tools of CNV dected
./CNV_pipeline/
.
├── extract_and_filter_Scripts
└── merge_cnvkit_res_Scripts

• As the reference data of human are much more sufficient than and mouse, this pipeline split into two parts. One of them is used on human data, and the other one is used on mouse data.
  • If you want use genomics piepline on human data, you could access the detail info by clicking here
  • If you want use genomics piepline on mouse data, you could access the detail info by clicking here