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 will perform comparably well in most applications. 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

realSFS method

make a consensus sequence (fasta) from one of the individuals

Here the *.list file contains paths to the bam files for NA19042. A separate consensus should be created for each chromosome. This step is optional, the reference sequence used for alignment can also be used.

{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

• .saf files are needed for each chromosome within each individual.

The *.list file contains paths to the bam files for NA19027. The file GEM_mappability1_75mer.angsd gives the sites passing the GEM mappability filter in, in a bed-like format required by ANGSD (see here: [2])

{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}

run realSFS for each pair of individuals

The command below runs realSFS for the NA19042 and NA19027. Run for each chromosome 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

IBS method

1. 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}

1. 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

1. Use the above R scripts to interpret the output of IBS and realSFS for each pair of individuals

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},
}