ANGSD: Analysis of next generation Sequencing Data
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Genotype Likelihoods: Difference between revisions
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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== | ==Genotype likelihoods from alignments== | ||
; -GL [int] | ; -GL [int] | ||
Revision as of 10:54, 19 June 2012
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
GATK
-GL 2
soapSNP
-GL 3