Introduction

transIndel is used to detect indels (insertions and deletions) from DNA-seq or RNA-seq data by parsing chimiric alignments from BWA-MEM.

Prerequisites

Samtools/1.0 or newer (http://www.htslib.org/) Python 3.6 or newer (https://www.python.org/) Python packages:

• Pysam/0.13.0 or newer (https://pypi.org/project/pysam)
• HTSeq/0.6.1 or newer (https://pypi.python.org/pypi/HTSeq)

Getting Soure Code

git clone git://github.com/cauyrd/transIndel.git
cd transIndel

Running transIndel

STEP 1: Build new BAM file with redefined CIGAR string

• analyzing DNA-seq data (whole genome seq/exome-seq/targeted capture)

  python transIndel_build_DNA.py -i input_bam_file -o output_bam_file [options]

• analyzing RNA-seq data

  python transIndel_build_RNA.py -i input_bam_file -r reference_genome_fasta -g gtf_file -o output_bam_file [options]

  Options:

  -h, –help show this help message and exit -i INPUT, –input INPUT

                    Input BAM file

  -o OUTPUT, –output OUTPUT

                    Output BAM file

  -r REF, –ref REF reference genome used for analyzing RNA-seq data -g GTF, –gtf GTF gene annotatino file used for analyzing RNA-seq data -s SPLICE_BIN, –splice_bin SPLICE_BIN

                    splice site half bin size (default: 20)

  -m MAPQ, –mapq MAPQ minimal MAPQ of read from BAM file for supporting

                    Indel (default: 15)

  -l LENGTH, –length LENGTH

                     Maximum deletion length to be detected (default:1000000)

  -v, –version show program’s version number and exit

Input:

input_bam_file               :input BAM file is produced by BWA-MEM and is sorted and indexed.
reference_genome_fasta (for RNA-seq)    :reference genome in FastA format
gtf_file (for RNA-seq)            :gene annotation file in GTF format

Output:

your_output_bam_file            :BAM file for CIGAR string redefinement.

transIndel generates the following optional fields in output BAMs

Tag| Meaning
--------------------------------------------------------------------------------------
OA | original representative alignment; format: (pos,CIGAR)
JM | splicing junction reads; infered from GTF or splicing motif (used in RNA-seq BAM)

STEP 2: Call indel

• Option 1: using transIndel_call.py script

  python transIndel_call.py -i input_bam_from_transIndel_build -o output_vcf_filename_prefix [options]    

  Options:

  -h, –help show this help message and exit -i INPUT, –input INPUT

                        Input BAM file

  -o OUTPUT, –output OUTPUT

                    output VCF file prefix

  -c AO, –ao AO minimal observation count for Indel (default: 4) -d DEPTH, –depth DEPTH

                 minimal depth to call Indel (default: 10)

  -f VAF, –vaf VAF minimal variant allele frequency (default: 0.1) -l LENGTH, –length LENGTH

                 minimal Indel length (>=1) to report (default: 10)

  -m MAPQ, –mapq MAPQ minimal MAPQ of read from BAM file to call Indel

                 (default: 15)

  -t REGION Limit analysis to targets listed in the BED-format

                 FILE or a samtools region string

  -v, –version show program’s version number and exit

Input:

input_bam_file               :input BAM file is produced by transIndel_build.py

Output:

output_vcf_file               :Reported Indels with VCF format

• Option 2: using existing variant caller (e.g. VarDict, freebayes, GATK)

  following the specific variant caller's manual