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LD Score Estimation Tutorial
This tutorial describes how to use ldsc to estimate LD Scores from plink format .bed/.bim/.fam filesets.
If you are interested in estimating genetic correlation or the LD Score regression intercept from European-ancestry GWAS data, you can download suitable pre-computed LD Scores from this URL; there is no need to compute your own LD Scores.
The tutorial is divided into two components. The first component describes how to estimate non-partitioned LD Scores. The second component describes how to estimate partitioned LD Scores and how to use the full baseline model from Finucane, Bulik-Sullivan et al., 2015. The second component is somewhat more complicated.
You can estimate HapMap3 LD Scores for chromosome 22 using genotype data from the 1000 Genomes Europeans by entering the following commands:
wget https://data.broadinstitute.org/alkesgroup/LDSCORE/1kg_eur.tar.bz2
tar -jxvf 1kg_eur.tar.bz2
python ldsc.py\
--bfile 22
--l2\
--ld-wind-cm 1\
--out 22
This section of the tutorial requires downloading about 2MB of data.
In order to estimate LD Scores, you need genotype data in the binary plink .bed/.bim/.fam format. We recommend using 1000 Genomes data from the appropriate continent, which can be downloaded in vcf format from the 1000 Genomes FTP site and converted to plink format using the plink --vcf command.
We recommend estimating LD Scores using a 1 centiMorgan (cM) window. Most .bim files have the cM column zeroed out, because plink doesn't actually use cM coordinates for anything. You can use the plink --cm-map flag along with your favorite genetic map (e.g., here) to fill in the cM column of your .bim file.
For the purpose of this tutorial, you can download a .bed/.bim/.fam fileset with the cM column filled in here. This fileset contains genotypes for all HapMap3 SNPs on chromosome 22 for 378 1000 Genomes Europeans. You can uncompress this fileset with the command
tar -jxvf 1kg_eur.tar.bz2
This will produce a directory called 1kg_eur with four files
22.bim
22.fam
22.bed
22.hm3.daf.gz
The first three files are the .bed/.bim/.fam fileset; the third file contains derived allele frequencies (DAFs) for all SNPs in the .bim file, for use with the ldsc --cts-bin flag later in the tutorial.
You can estimate LD Scores with the command
python ldsc.py\
--bfile\
--l2\
--ld-wind-cm 1\
--out 22
This should take around 10 seconds to run. The --bfile flag points to the plink format fileset; the syntax is exactly the same as plink. The --l2 flag tells ldsc to compute LD Scores. The --ld-wind-cm flag tells lsdc to use a 1 cM window to estimate LD Scores. The other options are --ld-wind-kb, which defines the window size in kilobases, and --ld-wind-snp, which defines the window size in terms of a number of SNPs. We recommend using --ld-wind-cm, because this allows the window size to vary with the range of LD. It is sensible to use a larger window (as measured in kb) in regions like the MHC where LD spans over tens of megabases than in regions with high recombination rate, where LD doesn't extend beyond ~100kb.
This command will produce four files:
22.log
22.l2.M
22.l2.M_5_50
22.l2.ldscore.gz
I will describe these files one at a time. First, let's have a look at the log file.
The first section is simply the masthead and a list of command-line options:
*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.0
* (C) 2014-2015 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Options:
--ld-wind-cm 1.0
--out 22
--bfile 22
--l2
The next section contains log messages describing the process of reading the .bed/.bim/.fam fileset. ldsc will remove monomorphic SNPs by default. You can change the MAF lower bound with the '--maf` flag.
Beginning analysis at Fri Jan 30 10:58:44 2015
Read list of 19156 SNPs from 22.bim
Read list of 379 individuals from 22.fam
Reading genotypes from 22.bed
After filtering, 19156 SNPs remain
Estimating LD Score.
Writing LD Scores for 19156 SNPs to 22.l2.ldscore.gz
The last section shows some basic metadata about the LD Scores. This section is useful for basic quality checks. For example, LD Score should generally be positively correlated with MAF. In this example, the correlation between MAF and L2 is 0.275, which seems sensible. Some LD Scores may be < 1, because ldsc estimates LD Score using an unbiased estimator of r2, but generally only a few LD Scores should be < 1. In this example, the mean LD Score is lower than usual, because we only took sum r2 over SNPs in HapMap3 to save time.
Summary of LD Scores in 22.l2.ldscore.gz
MAF L2
mean 0.232 18.535
std 0.145 16.104
min 0.001 0.066
25% 0.104 7.839
50% 0.224 13.484
75% 0.355 22.972
max 0.500 109.716
MAF/LD Score Correlation Matrix
MAF L2
MAF 1.000 0.275
L2 0.275 1.000
Analysis finished at Fri Jan 30 10:58:46 2015
Total time elapsed: 2.72s
Let's have a look at these files:
cat 22.l2.M 22.l2.M_5_50
19156
16885
These files tally the number of SNPs in the .bed/.bim/.fam fileset. The .M file contains the total number of SNPs; the .l2.M_5_50 file contains the number of SNPs with minor allele frequency above 5%. By default, ldsc uses the .l2.M_5_50 file for estimating heritability, because this avoids extrapolating that h2 per SNP among common variants is the same as for rare variants (see the Flavors of Heritability and Genetic Correlation subsection of the supplementary note of Bulik-Sullivan, Finucane, et al., 2015 for a more detailed explanation of this point). You can tell ldsc to use the .l2.M file with the --not-M-5-50 flag, but this will generally yield upwardly-biased h2 estimates.
ldsc compresses .l2.ldscore files by default using gzip. You can view the contents of this file by typing
gunzip -c 22.l2.ldscore.gz | head
CHR SNP BP L2
22 rs9617528 16061016 1.271
22 rs4911642 16504399 1.805
22 rs140378 16877135 3.849
22 rs131560 16877230 3.769
22 rs7287144 16886873 7.226
22 rs5748616 16888900 7.379
22 rs5748662 16892858 7.195
22 rs5994034 16894090 2.898
22 rs4010554 16894264 6.975
The first three columns are CHR = chromosome, SNP = rs number, BP = base pair. ldsc uses rs numbers for merging LD Score files with summary statistics, so don't worry if the BP column refers to an old genome build. The BP column is only used for making sure that SNPs are sorted. If you use ldsc to estimate LD Scores, the SNPs will always be sorted. The last column (L2) is LD Scores.
The LD Scores to use as the argument for the --w-ld and --w-ld-chr flags should be computed as sum r2 over SNPs in the regression, i.e., the SNPs for which you have Z-scores. If you have a list of regression SNPs in a file called regression.snplist, formatted as one rs number per line, no header, then you can compute the appropriate --w-ld LD Scores with the --extract regression.snplist flag (this is the same syntax for restricting to a subset of SNPs as in plink).
The --w-ld LD Scores are just used for weighting the regression and generally do not have a huge impact on the results. If you are using LD Score regression with a large number of traits have Z-scores for slightly different sets of SNPs for each trait, then we recommend using the same --w-ld LD Scores for each trait in order to save time.
To compute annotation-specific LD scores, you will need an annot file, with extension .annot or .annot.gz. An annot file typically consists of CHR, BP, SNP, and CM columns, followed by one column per annotation, with the value of the annotation for each SNP (0/1 for binary categories, arbitrary numbers for continuous annotations). The file can have many categories or just a single category. It must have the same SNPs in the same order as the .bim file used for the computation of LD scores. We also now allow for "thin annot" files, which omit the CHR, BP, SNP and CM columns and only have data on the annotation itself. The software assumes but does not check that thin annot files have the same SNPs in the same order as the plink files you used to compute LD scores. These require you to use the --thin-annot flag, as described below.
You can always create an annot file on your own. Make sure you have the same SNPs in the same order as the .bim file used for the computation of LD scores! We have simplified the annot file creation in two common cases: first, when an annotation consists of a set of genomic regions described in a UCSC bed file; and second, when an annot file is based on a gene set, as in Finucane et al. 2018 Nat Genet. In these two cases, you can use the script make_annot.py.
Note: this script outputs "thin annot" files. To compute LD scores from these files, you will need to use the flag --thin-annot, as below.
To use the make_annot.py script to compute annot files from a gene set, you will need the following inputs:
-
--gene-set-file, a gene set file with the names of the genes in your gene set, one line per gene name. -
--gene-coord-file, a gene coordinate file, with columns GENE, CHR, START, and END, where START and END are base pair coordinates of TSS and TES. This file can contain more genes than are in the gene set. We provide ENSG_coord.txt as a default. -
--windowsize, the window size you would like to use. The annotation will include all SNPs within this many base pairs of the transcribed region.
To compute annot files from a bed file, you will need the following inputs
-
--bed-file, the UCSC bed file with the regions that make up your annotation. -
--nomerge[rare]. Usually, you will not want to use this flag. Only use it if you do not want to merge the bed file; i.e., if you want to make a continuous annot file with values proportional to the number of intervals in the bedfile overlapping the SNP, rather than a binary annotation of SNPs that appear in any region.
In both cases, you will need the following inputs:
-
--bimfile, the plink bim file of the dataset you will use to compute LD scores. -
--annot-file, the name of the annot file to output. If this ends with.gzthen the resulting file will be gzip-ed.
To try out this script, download the sample files in this directory. You will also need 1000G.EUR.QC.22.bim in 1000G_Phase3_plinkfiles.tgz in this directory. Then run
python make_annot.py \
--gene-set-file GTEx_Cortex.GeneSet \
--gene-coord-file ENSG_coord.txt \
--windowsize 100000 \
--bimfile 1000G.EUR.QC.22.bim \
--annot-file GTEx_Cortex.annot.gz
or
python make_annot.py \
--bed-file Brain_DPC_H3K27ac.bed \
--bimfile 1000G.EUR.QC.22.bim \
--annot-file Brain_DPC_H3K27ac.annot.gz
Once you have annot file corresponding to 1000G.EUR.QC.22.bim---we will use the file Brain_DPC_H3K27ac.annot.gz created above---make sure you have 1000G.EUR.QC.22.bed and 1000G.EUR.QC.22.fam from 1000G_Phase3_plinkfiles.tgz, and also download HapMap3 SNPs (hm.22.snp in hapmap3_snps.tgz in this directory).
Then run
python ldsc.py\
--l2\
--bfile 1000G.EUR.QC.22\
--ld-wind-cm 1\
--annot Brain_DPC_H3K27ac.annot.gz\
--thin-annot
--out Brain_DPC_H3K27ac\
--print-snps hm.22.snp
(Note: the --thin-annot flag is only included if the annot file does not have the CHR, BP, SNP, and CM columns.) Repeat for the other chromosomes. Make sure you save your output files to the same directory, with the same file prefix, as your annot files, so that you have ${prefix}.${chr}.annot.gz, ${prefix}.${chr}.l2.ldscore, and ${prefix}.${chr}.l2.M_5_50.
Note that if you plan to use a comma-separated list of prefixes with the --ref-ld-chr flag, as in the "Cell-type group analysis" section of the Partitioning Heritability tutorial, then the two sets of LD scores must match in the sense of having the same set of SNPs that is in the baseline model. So if you are planning to build on top of the baseline model, be sure to use the files in 1000G_Phase3_plinkfiles.tgz, together with the HapMap3 SNPs, as above.