VarCal

Description

VarCal is a simple python script to call SNPs.

It takes BAM and reference fasta as input to call variants, which are reported in a tabular format.

Method

The tool can be run downloading the required environment file (env.yml) for conda and the pythin script (varcall.py).

The steps are given below:

$ conda env create -f env.yml 
$ conda activate varcall
$ python3 varcall.py -h
usage: varcall.py [-h] -b BAM -r REF -o OUT
Generate variant calls from a BAM file using ref fasta
optional arguments:
  -h, --help         show this help message and exit
  -b BAM, --bam BAM  bam file
  -r REF, --ref REF  reference fasta
  -o OUT, --out OUT  file name to output variant calls
 

Output columns

The output is a tab delimited text file and it has the following columns:

1. Chr - chromosome
2. POS - position of the variant
3. REF - Reference base
4. ALT - ALT base
5. Avg_BQ - Average base quality
6. Avg_MQ - Average mapping quality
7. Coverage - Read coverage
8. Avg_PiR - Average position of the base in the read
9. ALT_DP - Depth of alterate allele
10. AF - Allele frequency
11. Entropy - Entropy based on number of +ve and -ve strands
12. Total_Pos_Strand - Number of total reads mapped to +ve strand
13. Total_Neg_Strand - Number of total reads mapped to -ve strand

The following filters are applied by default:

1. Uniquely mapped reads only
2. Minimum total coverage of 5
3. Minimum variant-supporting coverage of 2
4. Minimum average base quality of q15
5. Minimum variant allele frequency of 0.01