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: Difference between revisions
| Line 17: | Line 17: | ||
===soapSNP=== | ===soapSNP=== | ||
-GL 3 | -GL 3 | ||
When estimating GL with soapSNP we need to generate a calibration matrix. This is done automaticly if these doesn't exist. | |||
These are located in angsd_tmpdir/basenameNUM.count,angsd_tmpdir/basenameNUM.qual | |||
<pre> | |||
../angsd0.3/angsd -bam CEU330.filelist -nInd 1 -GL 3 -doGlf 1 -out here -q 0 -ref /space/genomes/refgenomes/hg19/tsk/hg19.fa -r 20: | |||
</pre> | |||
This first loop doesn't estimate anything else than the calibration matrix. | |||
So now we can do the analysis we want | |||
<pre> | |||
../angsd0.3/angsd -bam CEU330.filelist -nInd 1 -GL 3 -out here -q 0 -ref /space/genomes/refgenomes/hg19/tsk/hg19.fa -r 20: -doGlf 3 | |||
</pre> | |||
===Kim et al.=== | ===Kim et al.=== | ||
Revision as of 11:37, 2 July 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 When estimating GL with soapSNP we need to generate a calibration matrix. This is done automaticly if these doesn't exist. These are located in angsd_tmpdir/basenameNUM.count,angsd_tmpdir/basenameNUM.qual
../angsd0.3/angsd -bam CEU330.filelist -nInd 1 -GL 3 -doGlf 1 -out here -q 0 -ref /space/genomes/refgenomes/hg19/tsk/hg19.fa -r 20:
This first loop doesn't estimate anything else than the calibration matrix. So now we can do the analysis we want
../angsd0.3/angsd -bam CEU330.filelist -nInd 1 -GL 3 -out here -q 0 -ref /space/genomes/refgenomes/hg19/tsk/hg19.fa -r 20: -doGlf 3