ldsc_real.md

This usecase describe how to run LDSC analysis (https://github.com/bulik/ldsc) on Morningness and Intelligence summary statistics data. All commands below assume that $SIF and $SINGULARITY_BIND environmental variables are defined as described in Getting started section of the main README file.

0. Assign the paths of the containers and reference data

export COMORMENT=/cluster/projects/p697/github/comorment
export SINGULARITY_BIND="$COMORMENT/containers/reference:/REF:ro"
export SIF=$COMORMENT/containers/singularity
export REP="rep${SLURM_ARRAY_TASK_ID}"
export EXTRACT="--extract /REF/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.$REP.snps"

1. The path of the summary statistics, name this path as 'sumstats_ld'

export sumstats_ld=$COMORMENT/containers/reference/sumstats

2. Uncompress sumstat data if required and copy these uncompressed sumstats to your working directory

gunzip $sumstats_ld/Morningness_sumstats_Jansenetal.txt.gz
unzip $sumstats_ld/SavageJansen_IntMeta_sumstats.zip

cp $sumstats_ld/Morningness_sumstats_Jansenetal.txt .

3. Arranging sumstats file for LDSC analysis via munge_sumstats.py

singularity exec --home $PWD:/home $SIF/ldsc.sif python /tools/ldsc/munge_sumstats.py \
--sumstats sumstats/SavageJansen_2018_intelligence_metaanalysis.txt \
--N  2000 \
--out int_munge \
--merge-alleles /REF/ldsc/w_hm3.snplist

singularity exec --home $PWD:/home $SIF/ldsc.sif python /tools/ldsc/munge_sumstats.py \
--sumstats Morningness_sumstats_Jansenetal.txt \
--out mor_munge \
--merge-alleles /REF/ldsc/w_hm3.snplist \
--signed-sumstats OR,0

4. remove .gz extension for munged sumstats

mv mor_munge.sumstats.gz mor_munge.sumstats
mv int_munge.sumstats.gz int_munge.sumstats

5. Ready to run LDSC analysis

singularity exec --home $PWD:/home $SIF/ldsc.sif python /tools/ldsc/ldsc.py  \
--rg int_munge.sumstats,mor_munge.sumstats \
--ref-ld-chr /REF/ldsc/eur_w_ld_chr/ \
--w-ld-chr /REF/ldsc/eur_w_ld_chr/ \
--out int_mor

The succesfull munge_sumstats.py and ldsc.py results shoud look like this:

Munge Intelligence:

Munge Morningness:

LDSC: