ANGSD: Analysis of next generation Sequencing Data
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Genotype Likelihoods: Difference between revisions
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===soapSNP=== | ===soapSNP=== | ||
-GL 3 | -GL 3 | ||
Anders destroyed an otherwise well working estimator | |||
===Kim et al.=== | ===Kim et al.=== | ||
-GL 4 | -GL 4 | ||
Thorfinn could not make it work | Thorfinn could not make it work | ||
[[Kim10|Citation]] [[Kim11|Citation]] | [[Kim10|Citation]] [[Kim11|Citation]] | ||
Revision as of 16:02, 22 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
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