Python package for identifying gene disrupting and restoring indels in whole-genome sequencing data of Mycobacterium tuberculosis samples
"Insertion" or "deletions" (affectionly called "indels") of nucleotides are two types of genetic changes besides single nucleotide polymorphims (SNPs) that can be detected by analyzing sequencing data. ScarTrek is an application written in python to detect indels in whole-genome sequencing data mapped to a reference genome, and if gene information for the referece organism is provided, then determine the genes that have the indels and if the indels influence the translated product of the gene. This analyses is useful to detect gene inactivations due to indels.
ScarTrek project can be downloaded directly from GitHub and python scripts can be run directly from the command line as shown in usage.
If downloaded from GitHub, ScarTrek can be run in the directory ScarTrek/scartrek/ as:
$ python find_scars.py [-h] -i INPUT [-m MAPRATE] [-c COVTHRES] [-q MAPQ] [-s SBALANCE] [-g GENESEQ] [-p PROTSEQ]
where the arguments are:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input directory that has mpileup files for each
sample. See tests/test1 for example (default: None)
-m MAPRATE, --maprate MAPRATE
Minimum read mapping rate required to consider a
sample (default: 20.0)
-c COVTHRES, --covthres COVTHRES
Minimum read coverage required at a position to detect
an indel (default: 20)
-q MAPQ, --mapq MAPQ Minimum average mapping quality required at a position
to detect an indel. This requires Samtools as well as
.bam and .bai files. Set this parameter to 0 if do not
want to use this filter. (default: 10)
-s SBALANCE, --sbalance SBALANCE
Minimum forward/reverse strand balance required at a
position to detect an indel (default: 0.05)
-g GENESEQ, --geneseq GENESEQ
Gene sequences in the reference genome, default
reference: M. tuberculosis (default:
../reference/H37Rv_genes.txt)
-p PROTSEQ, --protseq PROTSEQ
Protein sequences for the reference organism, default:
M. tuberculosis (default:
../reference/H37Rv_proteins_from_genbank.txt)
$ python find_scars.py -i ../example/ -q 0
The above example runs in <30 seconds. The MAPQ parameter is set to 0 (-q 0) because .bam and .bai files for the example are not included due to large file size.
ScarTrek has been tested on CentOS Linux 7 (Core) and Mac OS 10.13.5.