AntCaller

SNP calling and genotyping for damaged ancient DNA

Dependency

1. Python 2.7
2. samtools

Usage

1. This program is built on Python2.7 and can only be used for SAM/BAM files with MD field under Linux system.
2. Copy three .py files to the directory where SAM/BAM files are stored.
3. Print "python AntCaller-1.1.py -help" for detailed usage information.
4. SNP calling can only be performed after extracting damage information and pileuping reads.

Option

1. Default length of the longest reads in BAM file is set to 300. If there are reads that are longer than 300, "-l" option should be used in extracting damage information. For example, you can use "samtools view -h example.bam | python AntCaller-1.1.py --extract -l 600 -o example", if the longest reads are longer than 300bp but shorter than 600bp.

Examples

1. for BAM file (Require SAMtools installed)

1. pileup reads, output example.AntCaller.pileup

samtools view -h example.bam | python AntCaller-1.1.py --pileup -o example

2. extract damage information, output example.damageinfo

samtools view -h example.bam | python AntCaller-1.1.py --extract -o example

3. SNP calling, output vcf file

python AntCaller-1.1.py --snpcalling -o example -d example.damageinfo -f example.AntCaller.pileup

2. for SAM file

1. pileup reads, output example.AntCaller.pileup

cat example.sam | python AntCaller-1.1.py --pileup -o example

2. extract damage information, output example.damageinfo

cat example.sam | python AntCaller-1.1.py --extract -o example

3. SNP calling, output vcf file

python AntCaller-1.1.py --snpcalling -o example -d example.damageinfo -f example.AntCaller.pileup

Contact

For any problems, please contact boyanzhou1992@gmail.com