ANGSD: Analysis of next generation Sequencing Data

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Genotype Likelihoods

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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

Kim et al.

-GL 4 Citation Citation