모든 페이지
Configure공간 도구
메타데이터 끝으로 건너띄기
메타데이터 시작으로 이동하기
  • ADIscan Introduction

   

      1.Overview

        ADIScan1 (Allelic Depth and Imbalance Scanning)

        - Option 1 : Call variants by comparing the fractions of allelic reads in a tester to the universal reference genome.
        - Option 2 : Directly compare two sets of NGS data and predict discordant sequences based on allele fractions in two testers.

 

      2.License terms 


       ADIscan1 software is freely available for academic purposes and a license is required for commercial download and installation. 
       Please contact service@syntekabio.com for questions regarding the license

 


      3.Reference

       Cho, Lee, et al. (A manuscript is submitted.)

 

 

  • Manual

      1. COMMAND

        (1) Option1
            ./adi_scan –a [Bam file] -r [reference file]
        (2) Option2
           ./adi_scan –p [control Bam file] -q [case Bam file] -r [reference file]

 

       1.1. Options

        (1) Score cutoff(0~1) -z [double], default=0.5 using adiscan(1)
        (2) Score cutoff(1~50) -z [double], default=25 using adiscan(2)
        (3) Depth Cutoff -x [unsigned int], default=30 using variant caller
        (4) # of Thread -t [unsigned int], default=1
        (5) Detect Insert -i default=false
        (6) Detect Delete -d default=false
        (7) List File -l [list file], default= using filtering

      2. Example

       (1) Download reference : ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

       (2 )Variant Calling

          ./ADIscan1_r_v1.0 -a data/BLCA_ASN_N_860.bam -r [ref]

       (3) Somatic Calling

          ./ADIscan1_r_v1.0 -p data/BLCA_ASN_N_860.bam -q data/BLCA_ASN_T_860.bam -r [ref]

 

       Files : adiscan-test-set.tgz