ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
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