This repository contains code for SEQC2#WG3 project

Code

1_QC/                         ##Source codes for quality control of fastq files
2_Alignment_And_Calling/      ##Source codes for generating pipelines for each sample and generated shell file for each sample of various pipelines
3_vcfStat_and_DepthFilter/    ##Source codes for variant statistic by RTG tool and depth filtering by perl script 
4_Benchmarking/               ##Source codes for make final benchmark vcf and bed files
5_Reproducibility_Cal/        ##Source codes for calculation of reproducibility
6_PRF_Cal/                    ##Source codes for calculation of Precision/Recal/F-score
7_VarianceAnalysis/           ##description for detail of variance analysis

Reference Used:

GRCh38.d1.vd1 Reference Sequence:

https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files

Files for GATK recalibration:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/other_mapping_resources/Mills_and_1000G_gold_standard.indels.b38.primary_assembly.vcf.gz

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/other_mapping_resources/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz

ftp://[email protected]/bundle/hg38/dbsnp_146.hg38.vcf.gz

Prerequisites

x86_64-linux
Java (version > jdk1.8.0_91)
Perl (version >5.26.2)
R (version >3.6.1)
fastqc
bowtie2-2.2.9
bwa-0.7.15
isaac-01.15.04.01
stampy-1.0.29
GATK-3.7
picard-2.7.1
samtools-1.3.1
freeBayes-v1.1.0-1
samtools-1.3.1
bcftools-1.3.1
bedtools-2.28.0
SNVer-0.5.3
Varscan.v2.3.9