angsd - User contributions [en]

Filters

2012-09-24T11:15:26Z

Line: /* Selected Sites */

In most analysis you are only interested in a subset of sites and not all sites. Currently we have the following filter options.

=Selected Sites=

; -filter [bimfile.bim]: Return likelihoods for the positions in the .bim file. In addition the options -doMaf 2 -GL 1 must be provided. With -doMajorMinor 3 the major/minor alleles from the bim file is used.

=Allele frequencies=
; -minMaf [float]: only work with sites with a maf above 'float'

=polymorphic sites=

; -minLRT [float]: only work with sits with an LRT>float

=Major minor=
=Number of non missing individuals=

; -minKeepInd [int]: only work with sites with information from atleast int individiduals

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
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>

Now we do a filter with MAF cutoff of 1\%

<pre>
../angsd0.3/angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: -minMaf 0.01
head TSK.mafs
chromo position major minor knownEM nInd
1 13999950 T G 0.495291 2
1 14000019 G T 0.047247 9
1 14000056 C T 0.055851 10
1 14000127 G T 0.060760 10
1 14000170 C T 0.052388 9
1 14000176 G A 0.047928 10
1 14000202 G A 0.279722 9
1 14000262 C T 0.058555 9
1 14000322 A G 0.040471 8
</pre>

Similar if we only want sites with information for atleast 5 samples
<pre>
../angsd0.3/angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: -minKeepInd 5
head TSK.mafs
chromo position major minor knownEM nInd
1 13999971 T A 0.000007 6
1 13999972 G A 0.000007 6
1 13999973 C A 0.000005 5
1 13999974 G A 0.000006 6
1 13999975 C A 0.000002 5
1 13999976 C A 0.000004 7
1 13999977 A C 0.000005 8
1 13999978 C A 0.000005 8
1 13999979 T A 0.000005 8
</pre>
If we are interested in all sites with a p-value of 10^(-6) of being variable
<pre>
../angsd0.3/angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: -minLRT 24 -doSNP 1
head TSK.mafs
chromo position major minor knownEM pK-EM nInd
1 14000202 G A 0.279722 42.623150 9
1 14000873 G A 0.212120 79.118476 10
1 14001018 T C 0.333736 89.040311 8
1 14001867 A G 0.200232 47.195423 10
1 14002422 A T 0.167692 43.196259 9
1 14003581 C T 0.207404 58.593208 9
1 14004623 T C 0.219838 102.856433 10
1 14007493 A G 0.453217 28.398647 9
1 14007558 C T 0.395670 80.236777 7

</pre>

==Deprecated options==
These options should either be included (as is) or be discarded

;-minDepth:
;-maxDepth:

Filters

2012-09-24T11:13:35Z

Line: /* Selected Sites */

In most analysis you are only interested in a subset of sites and not all sites. Currently we have the following filter options.

=Selected Sites=

-filter [bimfile.bim]

In addition the options -doMaf 2 -GL 1 must be provided.

With -doMajorMinor 3 the major/minor alleles from the bim file is used.

=Allele frequencies=
; -minMaf [float]: only work with sites with a maf above 'float'

=polymorphic sites=

; -minLRT [float]: only work with sits with an LRT>float

=Major minor=
=Number of non missing individuals=

; -minKeepInd [int]: only work with sites with information from atleast int individiduals

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
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>

Now we do a filter with MAF cutoff of 1\%

<pre>
../angsd0.3/angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: -minMaf 0.01
head TSK.mafs
chromo position major minor knownEM nInd
1 13999950 T G 0.495291 2
1 14000019 G T 0.047247 9
1 14000056 C T 0.055851 10
1 14000127 G T 0.060760 10
1 14000170 C T 0.052388 9
1 14000176 G A 0.047928 10
1 14000202 G A 0.279722 9
1 14000262 C T 0.058555 9
1 14000322 A G 0.040471 8
</pre>

Similar if we only want sites with information for atleast 5 samples
<pre>
../angsd0.3/angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: -minKeepInd 5
head TSK.mafs
chromo position major minor knownEM nInd
1 13999971 T A 0.000007 6
1 13999972 G A 0.000007 6
1 13999973 C A 0.000005 5
1 13999974 G A 0.000006 6
1 13999975 C A 0.000002 5
1 13999976 C A 0.000004 7
1 13999977 A C 0.000005 8
1 13999978 C A 0.000005 8
1 13999979 T A 0.000005 8
</pre>
If we are interested in all sites with a p-value of 10^(-6) of being variable
<pre>
../angsd0.3/angsd -doMaf 2 -doMajorMinor 1 -out TSK -bam bam.filelist -GL 1 -r 1: -minLRT 24 -doSNP 1
head TSK.mafs
chromo position major minor knownEM pK-EM nInd
1 14000202 G A 0.279722 42.623150 9
1 14000873 G A 0.212120 79.118476 10
1 14001018 T C 0.333736 89.040311 8
1 14001867 A G 0.200232 47.195423 10
1 14002422 A T 0.167692 43.196259 9
1 14003581 C T 0.207404 58.593208 9
1 14004623 T C 0.219838 102.856433 10
1 14007493 A G 0.453217 28.398647 9
1 14007558 C T 0.395670 80.236777 7

</pre>

==Deprecated options==
These options should either be included (as is) or be discarded

;-minDepth:
;-maxDepth:

Depth

2012-09-21T14:24:59Z

Line: Created page with "Depth -doDepth 1 -doCount 1 Prints the frequencies of depths for each individual to .depth file. Options - maxDepth [int] Defaults to 100. Sites with more than maxDepth ..."

Depth

-doDepth 1 -doCount 1

Prints the frequencies of depths for each individual to .depth file.

Options

- maxDepth [int]

Defaults to 100.
Sites with more than maxDepth reads are counted as having 100 reads.

Output

The outputfile .depth has one line per individual, with maxDepth entries.