Revision as of 17:08, 18 June 2012

About

ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. All methods talk genotype uncertainty into account instead of basis the analysis on called genotypes. This is especially useful for low and medium depth data. The software is written in C++ and can handle thousands of samples

Overview of input and intermediary data

<classdiagram type="dir:LR"> [sequence data]->[genotype;likelihoods] [genotype;likelihoods]->[genotype;probabilities] [sequence files|bam files;SOAP files{bg:orange}]->[sequence data] [glf files|glfv3;soapSNP{bg:orange}]->[genotype;likelihoods] [genotype prob|beagle output{bg:orange}]->[genotype;probabilities] </classdiagram>

Analysis from sequencing data

<classdiagram> // [input|bam files;SOAP files{bg:orange}]->[sequence data]

[sequence data]->[output|summary stats;phat estimates;error estimates{bg:blue}]
</classdiagram>

Analysis from genotype likelihoods

<classdiagram> //[input data|glf files{bg:orange}]->[genotype;likelihoods] [genotype;likelihoods]->[output|glf files;beagle files;MAF estimates;MAF associations;SNP Calling;realSFS;error estimates;Inbreeding{bg:blue}]

</classdiagram>

Analysis from genotype probabilities

<classdiagram> //[input data|beagle output{bg:orange}]->[genotype;probabilities] [genotype;probabilities]->[output|genotype calling;MAF estimates;associations{bg:blue}]

</classdiagram>

Commands

gatk

angsd.g++ -outfiles samtools -GL 1 uppile -b ceu5.mapped.list soapsnp If no recalibration matrix exists these will be created first. angsd.g++ -outfiles soapsnp -GL 0 uppile -b ceu5.mapped.list gatk

angsd.g++ -outfiles gatk -GL 2 uppile -b ceu5.mapped.list

angsd.g++ -outfiles suyeon -doCounts 1 -qs 20 -doLike 1 uppile -b ceu5.mapped.list

Wish list

1. start stop to work with soap input (Not gonna happen I think)

@@ Line 58: / Line 58: @@
 angsd.g++ -outfiles suyeon  -doCounts 1 -qs 20 -doLike 1 uppile -b ceu5.mapped.list
 </code>
-=Possible Bugs=
-.18 If we don't get any reliable genotypelikelihoods for a site, the site wont be included in the .mafs file. If this is want we want I can't say.
-.20 the major minor, doesn't work for the 3genotypes likelihood format (beagle)
-.21 When using soap files do we want to infer major/minor from generated likes or from counts?
-.24 Should we plugin the keepInd vector for the realSFS
-angsd
-.02 modify the -doGeno to set -doMaf to avoid a segfault with pars->results->asso->freq
-.03 when dumping beagle we need to -doMaf 2 otherwise segfault
-.3 clean version with less features. The lost features will be reintroduced later.
 =Wish list=
 . start stop to work with soap input (Not gonna happen I think)

ANGSD: Difference between revisions