Angsd structure: Difference between revisions

Revision as of 18:33, 4 December 2013

History

Angsd started back in 2009 as a simple program for estimating allele frequency, based on this we incrementally added new functionality. A rough timeline can be found in the AUTHORS file in the program bundle

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 ==History==
-) A simple program to estimate the MAF based on files containing the counts of allleles (-doPhat). Used in (yu li 2009)
+Angsd started back in 2009 as a simple program for estimating allele frequency, based on this we incrementally added new functionality. A rough timeline can be found in the AUTHORS file in the program bundle
-) An implementation of (suyeon kim 2011). GL/error estimation based on counts of alleles along with proper GL MAF estimators and case/control association
-) 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.
-) 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.
-) The glfv3 reader from 4) was used to implement the score statistic of (skotte 2012).
-) The programs from 3) 4) 5) was merged. Program was still called dirtySoap
-) 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.
-) We made a native bam reader (inspired and based on the samtools program (heng li)) along with the GATK,soapSNP GL model.
-) The theta estimator along with the tajima was then implemented (almost submitted).

Angsd structure: Difference between revisions

Revision as of 18:33, 4 December 2013

History

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