peresay/vdjbase_pipeline repository overview

⁠VDJbase Pipeline

The geno-haplo processing pipeline for VDJbase⁠.

The pipeline contain four main scripts:

• vdjbase_pipeline.R⁠ pipelien script for cmd run
• constant_parameters_vdjbase.R⁠ constant parameters of the pipeline
• functions_tigger.R⁠ custom tigger functions
• collapse_seq.py⁠ collapse sequences script

⁠vdjbase-pipeline overview

The vdjbase-pipeline contains 5 sections:

1. Initial V(D)J alignment with IMGT reference set⁠, using IgBlast⁠ and MakeDb⁠ from change-o and a custom script⁠ for collapsing similar sequences.

2. Gene sampling and clonal inference using DefineClones⁠ from change-o. In this step it is possible to sample each gene for a representation of the repertoire. In VDJbase, for each V gene only 500 sequences (with D and J assignments) are sampled, and from these sequences, clones are inferred and one sequence per clone is taken for the downstream analysis.

3. Novel alleles inference using TIgGER findNovelAlleles⁠ with custom gene 5' end position. For each V gene, the 5' end position bound is set to the farthest position that is present in at least 95% of the annotated sequences. The potential novel alleles are then screened for a potential chimera event. The passed alleles are added to the germline reference and the repertoire is re-annotated.

4. Genotype inference using TIgGER inferGenotypeBayesian⁠ and creating a personal germline reference set. The repertoire is re-annotated and double chromosome deletions and haplotypes are inferred using RAbHIT deletionsByBinom and createFullHaplotype⁠.

5. OGRDB reports using ogrdbstats⁠.

⁠Docker version

A docker for the pipeline is available. The docker is based on the immcantation container⁠ with the added VDJbase pipeline.

⁠Docker

docker pull peresay/vdjbase_pipeline

⁠Using the Container

⁠Shell inside the container

Same as in immcantation container, you can invoke a shell using the following

docker run -it peresay/vdjbase_pipeline bash

⁠Sharing files with the container

Build in the same way as the immcantation container, the same four mount points are available:

/data
/scratch
/software
/oasis

⁠Geno-Haplo pipeline: vdjbase-pipeline

Runs the vdjbase-pipeline, the are several parameters that can be modified. For the full list please go to the help guide within the docker.

# Arguments
DATA_DIR=~/P1
FASTA_FILE=/data/P1_I1_S1.fasta
SAMPLE_NAME=P1_I1_S1
NPROC=4

# Run pipeline for all avialble parameters
docker run peresay/vdjbase_pipeline -h

# Run pipeline for fasta file in docker image
docker run -v $DATA_DIR:/data:z peresay/vdjbase_pipeline \
    vdjbase-pipeline -f $FASTA_FILE -s $SAMPLE_NAME -t $NPROC

AIRR_FILE=/data/P1_I1_S1.tsv
# Run pipeline for airr format file in docker image. 
docker run -v $DATA_DIR:/data:z peresay/vdjbase_pipeline \
    vdjbase-pipeline -f $AIRR_FILE -s $SAMPLE_NAME -t $NPROC 

⁠Tools and parameters

⁠Copying

VDJbase pipeline is free for use under the CC BY-SA 4.0