HTS (NGS) 関連のインフォマティクス情報についてまとめています。

可変数のタンデムリピート(VNTR)をジェノタイピングする adVNTR





Quick Start — adVNTR 1.1.1 documentation




本体 Github

#bioconda (link)
conda creatte -n advntr-env python=2.7
conda activate advntr-env
conda install -c bioconda -y advntr

advntr -h

$ advntr -h


adVNTR 1.3.3: Genopyting tool for VNTRs


Source code:




usage: advntr <command> [options]


Command: genotype find RU counts and mutations in VNTRs

         viewmodel view existing models in database

         addmodel add custom VNTR to the database

         delmodel remove a model from database


advntr: error: too few arguments

advntr genotype -h

 advntr genotype -h

usage: advntr genotype [options]


Input/output options:

  -a/--alignment_file <file>      alignment file in SAM/BAM/CRAM format

  -r/--reference_filename <file>  path to a FASTA-formatted reference file for CRAM files. It overrides

                                  filename specified in header, which is normally used to find the reference

  -f/--fasta <file>               Fasta file containing raw reads

  -p/--pacbio                     set this flag if input file contains PacBio reads instead of Illumina reads

  -n/--nanopore                   set this flag if input file contains Nanopore MinION reads instead of


  -o/--outfile <file>             file to write results. adVNTR writes output to stdout if oufile is not


  -of/--outfmt <format>           output format. Allowed values are {text, bed} [text]


Algorithm options:

  -fs/--frameshift                set this flag to search for frameshifts in VNTR instead of copy number.

                                  Supported VNTR IDs: [25561, 519759]

  -e/--expansion                  set this flag to determine long expansion from PCR-free data

  -c/--coverage <float>           average sequencing coverage in PCR-free sequencing

  --haploid                       set this flag if the organism is haploid

  -naive/--naive                  use naive approach for PacBio reads


Other options:

  -h/--help                       show this help message and exit

  --working_directory <path>      working directory for creating temporary files needed for computation

  -m/--models <file>              VNTR models file [vntr_data/hg19_selected_VNTRs_Illumina.db]

  -t/--threads <int>              number of threads [1]

  -u/--update                     set this flag to iteratively update the model

  -vid/--vntr_id <text>           comma-separated list of VNTR IDs





#pre-trained model

> ls -l vntr_data/

$ ls -l vntr_data/ 

total 44280

-rw-r--r--  1 kazuma  staff   9207808  3 22  2019 hg19_selected_VNTRs_Illumina.db

-rw-r--r--  1 kazuma  staff  13463552  3 22  2019 hg19_selected_VNTRs_Pacbio.db




mkdir log_dir
advntr genotype --vntr_id 301645 --alignment_file CSTB_2_5_testdata.bam --working_directory ./log_dir/


Targeted genotyping of variable number tandem repeats with adVNTR
Mehrdad Bakhtiari, Sharona Shleizer-Burko, Melissa Gymrek, Vikas Bansal, Vineet Bafna

Genome Research, 28(11), pp.1709-1719