SNP calling and genotyping for damaged ancient DNA
- Python 2.7
- samtools
- 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.
- 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.
- for BAM file (Require SAMtools installed)
- pileup reads, output example.AntCaller.pileup
samtools view -h example.bam | python AntCaller-1.1.py --pileup -o example
- extract damage information, output example.damageinfo
samtools view -h example.bam | python AntCaller-1.1.py --extract -o example
- SNP calling, output vcf file
python AntCaller-1.1.py --snpcalling -o example -d example.damageinfo -f example.AntCaller.pileup
- for SAM file
- pileup reads, output example.AntCaller.pileup
cat example.sam | python AntCaller-1.1.py --pileup -o example
- extract damage information, output example.damageinfo
cat example.sam | python AntCaller-1.1.py --extract -o example
- SNP calling, output vcf file
python AntCaller-1.1.py --snpcalling -o example -d example.damageinfo -f example.AntCaller.pileup
For any problems, please contact [email protected]