IBSrelate

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

IBS and realSFS are two methods implemented in ANGSD [1] that can be used to estimate the allele sharing "genotype distribution" for a pair of individuals. The paper describes and examines the differences between the two methods, but we expect they both comparably well. Below are links to two R scripts that can be used to load the output of IBS and realSFS and produce estimates of R0, R1 and KING-robust kinship.

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

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},
}