• numpy-1.11.0 (SciPy.org) https://pypi.python.org/pypi/numpy/1.11.0
• scipy-0.17.1 (SciPy.org) https://pypi.python.org/pypi/scikit-learn/0.17.1
• pandas-0.18.1 (pandas.pydata.org) https://pypi.python.org/pypi/pandas/0.18.1/
• python-dateutil-2.0 (pypi.python.org) http://labix.org/python-dateutil
• pytz-2016.4 (pypi.python.org) https://pypi.python.org/pypi/pytz/2016.4
• scikit-learn-0.17.1 (scikit-learn.org) https://pypi.python.org/pypi/scikit-learn/0.17.1
• pyrenn 0.1 (pyrenn.readthedocs.io) https://pyrenn.readthedocs.io/en/latest/

the user can check if s/he has any of these package/versions by running the python command:

pip list|grep package_name

  example: pip list|grep scipy

If any of these pacakges are not availble, it should be downloaded and installed before running SNP-ML. the user may use the following command to directly install a specific package:

pip install 'package==version'

  example: pip install 'numpy==1.11.0'

After downloading and extracting SNP-ML, the user probably needs to run chmod command if s/he has a permission issue, EXAMPLE: chmod 777 SNP-ML

1. samtools faidx reference.fa
2. samtools mpileup -g -f reference.fa genotype1.bam genotype2.bam genotype3.bam > output.bcf
3. bcftools call -vc -V indels output.bcf > output_snps.bcf
4. bcftools convert output_snps.bcf -o output_snps_input4snpml.vcf

  ./SNP-ML -i DNA_test.vcf -iM peanut_DNA -o output_test

  ./SNP-ML -i DNA_test.vcf -iM sim_peanut_two_10x -o output_test

  ./SNP-MLer -iTP TP_five_genotype_10x_snps.vcf -iFP FP_five_genotype_10x_snps.vcf -o sim_peanut_five_10x

NOTE: An extendable database is available (db), the user can donwload the desired database into the 'db' folder of SNP-ML.