ANGSD: Analysis of next generation Sequencing Data
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First we do a run with no filters | |||
<pre> | |||
./angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: | |||
... | |||
head TSK.mafs | |||
head TSK.mafs | |||
chromo position major minor knownEM nInd | |||
1 13999919 A C 0.000008 1 | |||
1 13999920 G A 0.000008 1 | |||
1 13999921 G A 0.000008 1 | |||
1 13999922 C A 0.000008 1 | |||
1 13999923 A C 0.000008 1 | |||
1 13999924 G A 0.000008 1 | |||
1 13999925 G A 0.000008 1 | |||
1 13999926 A C 0.000008 1 | |||
1 13999927 G A 0.000008 1 | |||
</pre> | |||
==Deprecated options== | ==Deprecated options== | ||
These options should either be included (as is) or be discarded | These options should either be included (as is) or be discarded | ||
Revision as of 13:58, 19 June 2012
In most analysis you are only interested in a subset of sites and not all sites. Currently we have the following filter options.
- -minMaf float
- only work with sites with a maf above 'float'
- -minKeepInd int
- only work with sites with information from atleast int individiduals
- -minLRT float
- only work with sits with an LRT>float
First we do a run with no filters
./angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: ... head TSK.mafs head TSK.mafs chromo position major minor knownEM nInd 1 13999919 A C 0.000008 1 1 13999920 G A 0.000008 1 1 13999921 G A 0.000008 1 1 13999922 C A 0.000008 1 1 13999923 A C 0.000008 1 1 13999924 G A 0.000008 1 1 13999925 G A 0.000008 1 1 13999926 A C 0.000008 1 1 13999927 G A 0.000008 1
Deprecated options
These options should either be included (as is) or be discarded
- -minDepth
- -maxDepth