antcaller's Introduction

AntCaller

SNP calling and genotyping for damaged ancient DNA

Dependency

Python 2.7
samtools

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.

Option

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

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

Contact

For any problems, please contact [email protected]

antcaller's People

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antcaller's Issues

Error creating pileup

I am running into issues creating a pileup from my bam file:

% samtools view -h my.bam | python AntCaller-1.1.py --pileup -o out

Traceback (most recent call last):
  File "AntCaller-1.1.py", line 70, in <module>
    temp_list.reverse()
AttributeError: 'range' object has no attribute 'reverse'

Thank you,
Y

SNP calling error

Traceback (most recent call last):
File "AntCaller_snpcalling.py", line 56, in
f1 = open(f1name, 'r')
IOError: [Errno 2] No such file or directory: '/data/analyses/paleogenomics/ancientprojects/4_antcaller/3.snp_calling/575_samples.temporary.pileup.3'
Traceback (most recent call last):
File "AntCaller_snpcalling.py", line 56, in
Traceback (most recent call last):
File "AntCaller_snpcalling.py", line 56, in
f1 = open(f1name, 'r')
IOError: [Errno 2] No such file or directory: '/data/analyses/paleogenomics/ancientprojects/4_antcaller/3.snp_calling/575_samples.temporary.pileup.4'
f1 = open(f1name, 'r')
IOError: [Errno 2] No such file or directory: '/data/analyses/paleogenomics/ancientprojects/4_antcaller/3.snp_calling/575_samples.temporary.pileup.2'
Traceback (most recent call last):
File "AntCaller_snpcalling.py", line 56, in
f1 = open(f1name, 'r')
IOError: [Errno 2] No such file or directory: '/data/analyses/paleogenomics/ancientprojects/4_antcaller/3.snp_calling/575_samples.temporary.pileup.5'
Traceback (most recent call last):
File "AntCaller-1.1.py", line 289, in
f2split = open(f2splitname, 'r')
IOError: [Errno 2] No such file or directory: '/data/analyses/paleogenomics/ancientprojects/4_antcaller/3.snp_calling/575_samples.vcf'