SNP calling and genotyping for damaged DNA
AntCaller
SNP calling and genotyping for damaged ancient DNA
Usage
- This program is built on Python2.7 and can only be used for SAM/BAM files with MD field under Linux system.
- Copy three .py files to the directory where SAM/BAM files are stored.
- Print "python AntCaller-1.1.py -help" for detailed usage information.
- SNP calling can only be performed after extracting damage information and pileuping reads.
Examples
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
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
To restore the repository download the bundle
wget https://archive.org/download/github.com-BoyanZhou-AntCaller_-_2018-04-20_06-50-33/BoyanZhou-AntCaller_-_2018-04-20_06-50-33.bundle
and run:
git clone BoyanZhou-AntCaller_-_2018-04-20_06-50-33.bundle
Source:
https://github.com/BoyanZhou/AntCallerUploader:
BoyanZhouUpload date: 2018-04-20