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The CallAllelesAB program is part of the genotyping of mutations pipeline of the Creation and Genomic Analysis of Irradiation Hybrids in Populus protocol.
Following the overall protocol, prior to this step a parsed mpileup file and parental SNP file must have already been created as input.

The programs CallAllelesAB.py and indel-allelic-ratio.py can be downloaded here.

The program CallAllelesAB.py uses parental allele information present in the parental SNP file to assign parental alleles to the samples as follows:

a. If only one allele type is present, and it is one of the parental alleles, that parental allele is assigned.
b. If two alleles are present, but the lesser represents less then 10% of the calls, the lesser allele is ignored and the more frequent one is treated as in (a)
c. If the two alleles are present and they both represent > 10% of the calls:
 i. If the two observed alleles correspond to the two parental alleles, the allele is called as a Het
 ii. In all other bi-allele cases with each greater than 10%, the genotype called is “na”

The parameters available for CallAllelesAB.py:
-s STR: Path to the input parental SNP file created in step 6.
-m STR: Path to the parsed pileup file
-o STR: This is the output file name.

Example command to run CallAllelesAB.py using the parental SNP file /data/p-SNPS.txt, the parsed pileup /data/parsed-result_mpileup.txt and the output file output.txt:

python2.6 /path/to/CallAllelesAB.py –s input-parental-SNPFile.txt –m create-parsed_mpileup.txt –o output_file_name.txt

The output has the following format:
Columns 1 through 5 are only present once. Columns 6 though 11 are present as many times as there are samples in the parsed-mpileup.txt file.
1. Chromosome / reference sequence name
2. Position in reference sequence
3. Chromosome / reference sequence nucleotide base.
4. Parental A allele from the SNP file
5. Parental B allele from the SNP file
6. SNP Type: This will be 1 if homozygous, and 2 if heterozygous
7. SNP1, the most common allele
8. SNP2, the second most common allele
9. Total coverage at that position
10. The percent parental allele A: This will be 1 if homozygous A, 0 is homozygous B, and 0.5 if heterozygous.
11. The coverage of the parental A allele.

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