indelConverter

Prerequisite

• docker (using biocontainers/samtools:1.3.1 to extract nucleotide from given position)
• Python 3
• corresponding referenece genome fasta

Installation

git clone https://github.com/shanghungshih/indelConverter.git

Acceptable format

• txt: tabular format (ex. database file from Annovar, note: it allows contig name without chr, ex. 1 10144 10145 TA T or chr1 10144 10145 TA T)
• vcf: vcf format

Parameters

• --in_file - input file
• --out_file - output file
• --in_reference - input corresponding reference fasta
• --type - input file type
• --to_dash - if true, convert indel in input file to format with '-' (ex. chr1 10144 10145 TA T to chr1 10144 10145 A -), else on the contrary

Quick start

Convert dash format to non-dash format for txt

python3 indelConverter.py --in_file data/dash.txt --in_reference /path/to/reference/ucsc.hg19.fasta --out_file data/out_dash.txt --type txt --to_dash false

Convert non-dash format to dash format for vcf (example file will be added in future, please use your own vcf file)

python3 indelConverter.py --in_file data/dash.vcf --in_reference /path/to/reference/ucsc.hg19.fasta --out_file data/out_dash.vcf --type vcf --to_dash true