Sites

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.

You should therefore limit your analyses to the chromosomes/scaffolds for which you have sites you want to analyse (beeing the chromsomes in your -sites file). This can be done with (assuming sites.txt is your -sites sites.txt file).

NB the positions are one indexed. Which means there should never be a position of zero.

cut -f1 sites.txt |sort|uniq |awk '{print $0":"}' >chrs.txt

And append -rf chrs.txt to your argument list.

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.

1. Either the user supply a file containing chromsome and positions
2. 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 filterfile

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

chr1  100001
chr1  2500000
chr1  347348

Example of augmented filterfile

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

1. filter.txt.bin
2. filter.txt.idx

Requirements

The file should be sorted according to column1. This can be achieved by:

sort -k1 unsorted.txt >sorted.txt