SNP calling

SNP Calling

Likelihood ratio test

SNPs are called based on their allele frequencies. If a site has a minor allele frequency significantly different from 0 a site i called as polymorphic. The MAF estimate(s) given by -doMaf (see Allele_Frequency_estimation), will be used for a like ratio test by using a chi-square distribution with 1df for -doMaf 1 and 3df for -doMaf 3.

options

-SNP_pval [float]

The p-value used for calling snaps. see Allele_Frequency_estimation for additional options

example

In this example we analyse data from bam files (-bam bam.files), calculate the genotype likelihood using the samtools method (-GL 1), infer the major and minor alleles (-doMajorMinor 1), estimate the allele frequencies assuming known minor (-doMAF 2) and only keep those sites that have a p-value of 1e-6 for being variable.

./angsd -bam bam.filelist -GL 1 -out outfile -doMaf 2 -SNP_pval 1e-6 -doMajorMinor 1

output

the results are given in the file outfile.mafs:

chromo  position        major   minor   knownEM pK-EM   nInd
1       14008260        C       A       0.000001        -0.000074       32
1       14008261        A       C       0.000000        -0.000051       31
1       14008262        G       T       0.000001        -0.000099       32
1       14008263        C       A       0.000001        -0.000093       32
1       14008264        A       T       0.000010        -0.000574       32
1       14008265        T       C       0.000001        -0.000144       31
1       14008266        G       A       0.000000        -0.000049       31
1       14008267        G       A       0.000001        -0.000100       31
1       14008268        G       A       0.000001        -0.000081       30
1       14008269        G       A       0.168397        191.962068      31
1       14008270        G       A       0.000001        -0.000075       31
1       14008271        A       C       0.000001        -0.000109       31
1       14008272        A       C       0.000001        -0.000081       29
1       14008273        A       C       0.000002        -0.000156       30

The colums are the chromosome, the position, the major allele, the minor allele, the minor allele estimate, the likelihood ratio statistic and the number of individuals with information. In this example one site has a high likelihood ratio statistic.