BWA-GATK Version 1.0
Pipeline from sequencing reads to visualization of VCF. The eGPS provides a number of useful pipelines, including sequencing reads (after quality control) mapping, duplicates marking, single nucleotide polymorphisms and small indel variation can be called from population sequencing data.
Input Parameters
How to cite
[1] Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]
[2] Mckenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data[J]. Genome Research, 2010, 20(9):1297-303.[PMID: 20644199]
Help information

Version 1.0
Usage: -s -f -k -in1 -in2
opts :
-s      sample name
-f      reference file name
-k      known site (dbsnp file)
-in1    fastq1
-in2    fastq2

Parameters Description
-S: Sample_name
sample name
-F: Reference file  name
reference species name
-K: Known site 
if you choose human,dbsnp vcf file available; else it can be empty
-in1: Fastq1
fastq file 1
-in2: Fastq2
fastq file 2
  • Strategic Priority Research Program of the Chinese Academy of Sciences,Grant No. XDB13000000
    Maintained by BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences.