
thorfinn Sand 12/12/12 thorfinn@binf.ku
anders albrechtsen 12/12/12 albrecht@binf.ku.dk

Angsd is the process of the merging of different programs, below is a short description.


1) A simple program to estimate the MAF based on files containing the counts of allleles (-doPhat). Used in (yu li 2009)

2) An implementation of (suyeon kim 2011). GL/error estimation based on counts of alleles along with proper GL MAF estimators and case/control association

3) To perform genomewide analysis a .soap file was reader was made and this was merged with 1) and 2). At this time the program was called 'dirtySoap'. Name was choosen, since it was a hack that used soap files.

4) A program called realSFS (nielsen 2012) to estimate the SFS was implemented and used text representation of glfv3. This was extended to read glfv2 and binary glv3.

5) The glfv3 reader from 4) was used to implement the score statistic of (skotte 2012).

6) The programs from 3) 4) 5) was merged. Program was still called dirtySoap

7) We extended the dirtySoap with the mpileup reading from samtools 1.17 and called the program angsd. This was implemented with the samtool beeing invoked from inside angsd.

8) We made a native bam reader (inspired and based on the samtools program (heng li)) along with the GATK,soapSNP GL model.

9) The theta estimator along with the tajima was then implemented (almost submitted).


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The website 'http://www.popgen.dk/angsd' is the main resource for this program
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Some source files in this program hasn't been written by us bare have been taken from other opensource/public domain projects.


1)
k*.* files are from the klib which is written by heng li

2)
the files fet,razip,bgzf,faidx are full unmodified copies, copyright etc can be found in the header of those files.

3)
soap_likes.*, contains snippets of code from the SNPsoap package
bams.*,baq_adjustMapQ  contains snippets of code from the 'SAMtools' project.


Don't hesitate to contact us if you believe there are problems with copyright or somebody should be credited

Thorfinn Sand Korneliussen
thorfinn@binf.ku.dk
29 june 2014


