IBSrelate: Difference between revisions
No edit summary |
No edit summary |
||
Line 41: | Line 41: | ||
-nInd 5 -allpairs 1 \ | -nInd 5 -allpairs 1 \ | ||
-outFileName ./data/1000G_aln/GLF/chromosomes/chr{CHR}.model0 | -outFileName ./data/1000G_aln/GLF/chromosomes/chr{CHR}.model0 | ||
# Use R scripts to interpret the output of IBS and realSFS | |||
</pre> | </pre> | ||
Revision as of 18:21, 4 December 2018
Overview
This page contains information about the method IBSrelate, a method to identify relatives without requiring population allele frequencies. Here we show you how to estimate the R0, R1 and KING-robust kinship statistics for a pair (or more!) of individuals from aligned sequencing data. These statistics are informative about relatedness, but can also be useful for quality-control (QC). For details please see our paper in Molecular Ecology at: https://doi.org/10.1111/mec.14954
Calculating statistics from the output of IBS and realSFS
https://github.com/rwaples/freqfree_suppl/blob/master/read_IBS.R
https://github.com/rwaples/freqfree_suppl/blob/master/read_realSFS.R
Example Usage
# make consensus - needed to make saf files {ANGSD} -b ./data/1000G_aln/NA19042.mapped.ILLUMINA.bwa.LWK.low_coverage.20130415.list \ -r {CHR} -minMapQ 30 -minQ 20 -setMinDepth 3 -doFasta 2 -doCounts 1 -out ./data/consensus.NA19042.chr{CHR} # make *.saf files (per individual) {ANGSD} -b ./data/1000G_aln/NA19027.mapped.ILLUMINA.bwa.LWK.low_coverage.20130415.list \ -r {CHR} \ -ref ./data/1000G_aln/hs37d5.fa \ -anc ./data/consensus.NA19042.chr{CHR}.fa.gz \ -sites ./data/1000G_aln/GEM_mappability1_75mer.angsd \ -minMapQ 30 -minQ 20 -GL 2 \ -doSaf 1 -doDepth 1 -doCounts 1 \ -out ./data/1000G_aln/saf/chromosomes/NA19027_chr{CHR} # realSFS for each pair of individuals {realSFS} ./data/1000G_aln/saf/chromosomes/NA19042_chr{CHR}.saf.idx ./data/1000G_aln/saf/chromosomes/NA19027_chr{CHR}.saf.idx -r {CHR} -P 2 -tole 1e-10 > ./data/1000G_aln/saf/chromosomes/NA19042_NA19027_chr{CHR}.2dsfs # make genotype likelihood file {ANGSD} -b ./data/1000G_aln/bamlist.all.txt \ -r {CHR} \ -sites ./data/1000G_aln/GEM_mappability1_75mer.angsd \ -minMapQ 30 -minQ 20 -GL 2 \ -doGlf 1 \ -out ./data/1000G_aln/GLF/chromosomes/chr{CHR} # IBS {IBS} -glf ./data/1000G_aln/GLF/chromosomes/chr{CHR}.glf.gz \ -seed {CHR} -maxSites 300000000 -model 0 \ -nInd 5 -allpairs 1 \ -outFileName ./data/1000G_aln/GLF/chromosomes/chr{CHR}.model0 # Use R scripts to interpret the output of IBS and realSFS
Citation
Waples, R. K., Albrechtsen, A. and Moltke, I. (2018), Allele frequency‐free inference of close familial relationships from genotypes or low depth sequencing data. Mol Ecol. doi:10.1111/mec.14954
Bibtex
@article{doi:10.1111/mec.14954, author = {Waples, Ryan K and Albrechtsen, Anders and Moltke, Ida}, title = {Allele frequency-free inference of close familial relationships from genotypes or low depth sequencing data}, journal = {Molecular Ecology}, volume = {0}, number = {ja}, pages = {}, doi = {10.1111/mec.14954}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/mec.14954}, eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.14954}, }