AntCaller

SNP calling and genotyping for damaged ancient DNA

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.

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

wget https://archive.org/download/github.com-BoyanZhou-AntCaller_-_2018-04-20_06-50-33/BoyanZhou-AntCaller_-_2018-04-20_06-50-33.bundle

 git clone BoyanZhou-AntCaller_-_2018-04-20_06-50-33.bundle 

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