This page describes the -sites filtering that angsd allows. This functionality allows the user to supply a list of sites for which the analysis will be limited to. If you are interested in regions you should consider to use the -r/-rf options, as described in Filters. The -sites will loop over all input data, where as the -r/-rf, will use the indexing of BAM files. The -sites and -r/-rf can be used in combination.

Brief overview

/angsd -sites 
	-> angsd version: 0.569	 build(Dec 11 2013 13:38:47)
	-> Analysis helpbox/synopsis information:
--------------
analysisKeepList.cpp:
	-sites		(null)	(File containing sites to keep (chr tab pos))
	-minInd		0	Only use site if atleast minInd of samples has data
	You can force major/minor by -doMajorMinor 3
	And make sure file contains 4 columns (chr tab pos tab major tab minor)

Details

-sites filename

File containing the sites to include in analysis. If the site does not exist in the sequencing data, then the sites will of course not be included in the output.

-minInd [int]

Only keep those sites where we have data for at least this number of individuals.

We support 2 different kinds of inputfiles for filtering.

Either the user supply a file containing chromsome and positions
Or the user supply a file containing chromosome,position, major and minor

Only sites contained in the filter file will be outputted. If you supply an augmented filter for the purpose of forcing a major and minor state then remember to supply '-doMajorMinor 3'

A filter file is supplied to ANGSD with the command

-filter filename

Example of a filter file. File must be tab seperated.

chr1  100001
chr1  2500000
chr1  347348

Example of a file containing information of major and minor. File must be tab seperated.

1	728951	T	C
1	752721	A	G
1	754182	A	G
1	754334	T	C
1	760912	C	T
1	776546	G	A
1	779322	G	A
1	838555	A	C

The major and minor state can also be encoded as 0,1,2,3,4. With 0=A,1=C,2=G,3=T,4=N

We do not require the positions to be sorted, but we require that the file is grouped by chromosome name.

Internal representation

if a filter file has been supplied as '-filter filter.txt', then ANGSD will parse the entire filter.txt file and generate binary representations and dump these in the outputfiles called

filter.txt.bin
filter.txt.idx

Therefore remember to purge old versions of these files, if you have updated the filter.txt file.

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

Number of non missing individuals

-minInd [int]: only work with sites with information from atleast int individiduals, requires -doCounts 1

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 
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

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

../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

Similar if we only want sites with information for atleast 5 samples

../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

If we are interested in all sites with a p-value of 10^(-6) of being variable

../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

Deprecated options

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

-minDepth
-maxDepth

Sites

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