Last updated: 2013/3/5


GAP5_SNP is for detecting SNPs and GAP5_INDEL is for detecting small insertions and deletions
in a genome using pair-end sequencing.


Here we show how to use GAP5_SNP or GAP5_INDEL.


A. Uncompress tar.gz file

   tar -xvfz staden-2.0.0b9.tar.gz

B. Configure environment.

  cd staden-2.0.0b9-src/build.myhost
  ../configure --prefix=the directory where staden-2.0.0b9 is installed
  make
  make install

C. Run GAP5_SNP or GAP5_INDEL

1. Preparation

(1) Map reads on the reference genome using mapping software. 
    The mapped file is in SAM format and should be sorted by chromosome and position.

(2) Index the SAM file for GAP5
    
    staden-2.0.0b9/bin/tg_index -o <gap5_file_name> <SAM_file_name>
    
2. Run GAP5_SNP

    staden-2.0.0b9/bin/gap5_snp -out <SNP_file_name.vcf> -ref <reference file> gap5_file_name
    
3. Run GAP5_INDEL

    staden-2.0.0b9/bin/gap5_indel -out <INDEL_file_name.vcf> -ref <reference file> gap5_file_name

D. Results format is VCF.