|
|
| (126 intermediate revisions by 2 users not shown) |
| Line 1: |
Line 1: |
| =Brief description= | | = NEW VERSION = |
| This page contains information about the program called NgsRelate, which can be used to infer relatedness coefficients for pairs of individuals for low coverage nags data by using genotype likelihoods. To be able to infer the relatedness you will need to know the population frequencies and have genotype likelihoods. This can be done e.g. using the program ANGSD as shown in the example.
| | For the NEW version of ngsRelate that coestimates relatedness and inbreeding go to this link https://github.com/ANGSD/NgsRelate |
|
| |
|
| =Installation=
| |
| Primary repository is github. https://github.com/ANGSD/NgsRelate
| |
| == Download Installation of C program ==
| |
| <pre>
| |
| curl https://raw.githubusercontent.com/ANGSD/NgsRelate/master/NgsRelate.cpp >NgsRelate.cpp
| |
| g++ NgsRelate.cpp -O3 -lz -o NgsRelate
| |
| </pre>
| |
|
| |
|
| = Run example using C = | | = OLD VERSION = |
| Assume we have file containing paths to 100 BAM/CRAM files, then we can use ANGSD to estimate frequencies calculate genotype likelihoods while doing SNP calling and dumping the input files needed for the NgsRelate program
| | For the old version please use this link: http://www.popgen.dk/software/index.php?title=NgsRelate&oldid=694 |
| <pre>
| |
| ./angsd -b filelist -gl 1 -domajorminor 1 -snp_pval 1e-6 - domaf 1 -minmaf 0.05 -doGlf 3
| |
| #this generates an angsdput.mafs.gz and a angsdput.glf.gz.
| |
| #we will need to extract the frequency column from the mafs file and remove the header
| |
| cut -f5 angsdput.mafs.gz |sed 1d >freq
| |
| ./ngsrelate -g angsdput.glf.gz -n 100 -f freq -a 0 -b 1 >gl.res
| |
| </pre>
| |
| Here we specify that our binary genotype likelihood file contains 100 samples, and that we want to run the analysis for the first two samples -a 0 -b 1.
| |
| If no -a and -b are specified it will loop through all pairs
| |
| | |
| == Output file format==
| |
| Example of output
| |
| <pre>
| |
| Pair k0 k1 k2 loglh nIter coverage
| |
| (0,1) 0.673213 0.326774 0.000013 -1710940.769941 19 0.814658
| |
| </pre>
| |
| | |
| | |
| The first two columns are the individuals number. The next three columns are the estimated relatedness coefficients and the last column is the number of iterations used.
| |
| | |
| | |
| = Input file format = | |
| The input files are binary gz compressed, log like ratios encoded as double. 3 values per sample.
| |
| The freq file is allowed to be gz compressed.
| |
| | |
| = Citing and references = | |
| | |
| = Changelog =
| |
| See github for log
| |