Vcall

We build a variant calling tool specifically on SNPs, and could expand to more later. Use Vcallsnp to perform variant calling on SNPs.

Installation instructions

Installation requires pandas to be installed. You can install it using pip:

pip install pandas 

Installation requires numpy to be installed. You can install it using pip:

pip install numpy 

Installation requires scipy to be installed. You can install it using pip:

pip install scipy

Once you have all packages installed, please download the Vcall folder and the setup.py file and put the setup.py in the same directory with the Vcall fole, then open a terminal and cd to the directory. Finally, you can install Vcall using pip:

pip install .

note: detailed version is in requirements.txt.

Basic Usage

usage:

Vcallsnp [-h] [-mvf MINVARFREQ] [-mc MINCOVERAGE] [-mr MINREADS] [-maq MINAVGQUAL] [-mffh MINFREQFORHOM] [-p PVALUE] [-sf STRANDFILTER] [-out OUTPATH] [-f FILENAME] MPILEUPFILE

To run mypileup on a small test example (using files in this repo):

Vcallsnp ./test/trio.mpileup -mvf 0.2 -mffh 0.8 -p 0.01 -f filename

Options

positional arguments:

• MPILEUPFILE path to the input mpileup file

• -op OUTPATH, --out-path OUTPATH Specify the output path (default: current working directory)

• -o OUTPUT, --output OUTPUT Specify the output file name (default: output)

optional arguments:

• -h, --help show this help message and exit

• -mvf MINVARFREQ, --min-var-freq MINVARFREQ minimum frequency threshold for variants (default: 0.2)

• -mc MINCOVERAGE, --min-coverage MINCOVERAGE Minimum read depth at a position to make a call (default: 8)

• -mr MINREADS, --min-reads MINREADS Minimum supporting reads at a position to call variants (default: 2)

• -maq MINAVGQUAL, --min-avg-qual MINAVGQUAL Minimum base quality at a position to count a read (default: 15)

• -mffh MINFREQFORHOM, --min-freq-for-hom MINFREQFORHOM Minimum frequency to call homozygote (default: 0.75)

• -p PVALUE, --p-value PVALUE p-value threshold for calling variants (default: 0.99)

• -sf STRANDFILTER, --strand-filter STRANDFILTER Ignore variants with more than 90 percent support on one strand (default: True)

File format

The input file format is mpileup, generated by samtools using bam file.

The output file will be in VCF.

Contributors:

Kaifu Yang and Jiayu Chen developed this tool, with inspiration from VarScan and lab1 from CSE 185 at UCSD.

Email for questions regarding the tool:

Kaifu Yang: [email protected]

Jiayu Chen: [email protected]