Genotype Likelihoods

Analysis from sequencing data

<classdiagram> // [input|bam files;SOAP files{bg:orange}]->[sequence data]

[sequence data]->[genotype likelihoods|samtools;GATK;soapSNP;kim et.al]
</classdiagram>

Genotype likelihoods from alignments

-GL [int]

If your input is sequencing file you can estimate genotype likelhoods from the mapped reads. Four different methods are available.

Samtools

-GL 1

This methods has a random component. To get the exact same results as samtools use nThreads=1.

GATK

-GL 2

soapSNP

-GL 3 When estimating GL with soapSNP we need to generate a calibration matrix. This is done automaticly if these doesn't exist. These are located in angsd_tmpdir/basenameNUM.count,angsd_tmpdir/basenameNUM.qual

../angsd0.3/angsd -bam CEU330.filelist -nInd 1 -GL 3 -doGlf 1 -out here -q 0 -ref /space/genomes/refgenomes/hg19/tsk/hg19.fa -r 20:

This first loop doesn't estimate anything else than the calibration matrix. So now we can do the analysis we want

../angsd0.3/angsd -bam CEU330.filelist -nInd 1 -GL 3 -out here -q 0 -ref /space/genomes/refgenomes/hg19/tsk/hg19.fa -r 20: -doGlf 3

Kim et al.

-GL 4 Anders destroyed another estimator Citation Citation