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 Anders destroyed an otherwise well working estimator

Kim et al.

-GL 4 Thorfinn could not make it work Citation Citation