Polygenic score examples

Examples

Examples

Most of the following examples show how to process summary statistics mostly made available through the Psychiatric Genomics Consortium (PGC) and generate polygenic score loadings

Attention Deficit Hyperactivity Disorder

Download ADHD summary statistics 2018 ADHD, 2019 ADHD and 2023 ADHD studies

wget -O ADHD_female.GCST012597_buildGRCh37.tsv.gz https://figshare.com/ndownloader/files/35310529
wget -O ADHD_male.GCST005362_buildGRCh37.tsv.gz https://figshare.com/ndownloader/files/35310532
wget -O daner_adhd_meta_filtered_NA_iPSYCH23_PGC11_sigPCs_woSEX_2ell6sd_EUR_Neff_70.meta.gz https://figshare.com/ndownloader/files/28169253
wget https://ipsych.dk/fileadmin/iPSYCH/PGC/ADHD_meta_Jan2022_iPSYCH1_iPSYCH2_deCODE_PGC.meta_2.zip

for pfx in female.GCST012597 male.GCST005362; do
  zcat ADHD_${pfx}_buildGRCh37.tsv.gz | cut -f1-3,6- |  sed '1 s/orig_//g' | \
  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s ADHD_${pfx%.GCST0[01][25][35][69][27]}_2018 | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o ADHD_$pfx.hg38.bcf -Ob --write-index
done

bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s ADHD_2019 \
  daner_adhd_meta_filtered_NA_iPSYCH23_PGC11_sigPCs_woSEX_2ell6sd_EUR_Neff_70.meta.gz | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o ADHD_2019.hg38.bcf -Ob --write-index

unzip -p ADHD_meta_Jan2022_iPSYCH1_iPSYCH2_deCODE_PGC.meta_2.zip \
  ADHD_meta_Jan2022_iPSYCH1_iPSYCH2_deCODE_PGC.meta.gz | \
bcftools +munge -C colheaders.tsv -f human_g1k_v37.fasta -s ADHD_2023 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o ADHD_meta_Jan2022_iPSYCH1_iPSYCH2_deCODE_PGC.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 1e-7 \
  --max-alpha-hat2 8e-4 \
  --exclude 'FILTER="IFFY"' \
  ADHD_meta_Jan2022_iPSYCH1_iPSYCH2_deCODE_PGC.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output ADHD_meta_Jan2022_iPSYCH1_iPSYCH2_deCODE_PGC.hg38.pgs.b1e-7.bcf \ 
  --output-type b \
  --log ADHD_meta_Jan2022_iPSYCH1_iPSYCH2_deCODE_PGC.hg38.pgs.b1e-7.log \
  --write-index

Anxiety Disorder

Download ANX summary statistics from 2019 ANX study

wget -O pgc-panic2019.vcf.tsv.gz https://figshare.com/ndownloader/files/30731276

zcat pgc-panic2019.vcf.tsv.gz | sed '/\t$/d' | \
bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s ANX_2019 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o pgc-panic2019.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 2e-7 \
  --max-alpha-hat2 0.008 \
  --exclude 'FILTER="IFFY"' \
  pgc-panic2019.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output pgc-panic2019.hg38.pgs.b2e-7.bcf \
  --output-type b \
  --log pgc-panic2019.hg38.pgs.b2e-7.log \
  --write-index

Autism Spectrum Disorder

Download ASD summary statistics from 2019 ASD study

wget -O iPSYCH-PGC_ASD_Nov2017.gz https://figshare.com/ndownloader/files/28169292

bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s ASD_2017 --ns 46351 --nc 18382 iPSYCH-PGC_ASD_Nov2017.gz | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o ASD_Nov2017.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 1e-7 \
  --max-alpha-hat2 8e-4 \
  --exclude 'FILTER="IFFY"' \
  ASD_Nov2017.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output ASD_Nov2017.hg38.pgs.b1e-7.bcf \
  --output-type b \
  --log ASD_Nov2017.hg38.pgs.b1e-7.log \
  --write-index

Bipolar Disorder

Download BIP summary statistics from 2021 BIP study

wget -O pgc-bip2021-all.vcf.tsv.gz https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/26603681/pgcbip2021all.vcf.tsv.gz
wget -O pgc-bip2021-BDI.vcf.tsv.gz https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/26603690/pgcbip2021BDI.vcf.tsv.gz
wget -O pgc-bip2021-BDII.vcf.tsv.gz https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/26603702/pgcbip2021BDII.vcf.tsv.gz

for pfx in all BDI BDII; do
  zcat pgc-bip2021-$pfx.vcf.tsv.gz | sed '/\t$/d' | \
  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s BIP_2021_$pfx | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o pgc-bip2021-$pfx.hg38.bcf -Ob --write-index

  bcftools +pgs \
    --no-version \
    --beta-cov 2e-7 \
    --max-alpha-hat2 0.001 \
    --exclude 'FILTER="IFFY"' \
    pgc-bip2021-$pfx.hg38.bcf \
    1kg_ldgm.EUR.bcf \
    --output pgc-bip2021-$pfx.hg38.pgs.b2e-7.bcf \
    --output-type b \
    --log pgc-bip2021-$pfx.hg38.pgs.b2e-7.log \
    --write-index
done

Anorexia Nervosa

Download AN summary statistics from 2019 AN study

wget -O pgcAN2.2019-07.vcf.tsv.gz https://figshare.com/ndownloader/files/28169271

bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s AN_2019 pgcAN2.2019-07.vcf.tsv.gz | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o pgcAN2.2019-07.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 2e-7 \
  --max-alpha-hat2 0.001 \
  --exclude 'FILTER="IFFY"' \
  pgcAN2.2019-07.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output pgcAN2.2019-07.hg38.pgs.b2e-7.bcf \
  --output-type b \
  --log pgcAN2.2019-07.hg38.pgs.b2e-7.log \
  --write-index

Major Depressive Disorder

Download MDD summary statistics from 2021 MDD study (samples sizes estimated from eTable2)

wget -O jamapsy_Giannakopoulou_2021_exclude_whi_23andMe.txt.gz https://figshare.com/ndownloader/files/31424374
wget -O jamapsy_Giannakopoulou_2021_exclude_whi_23andMe_ukb.txt.gz https://figshare.com/ndownloader/files/34437842

for pfx in 23andMe{,_ukb}; do
  if [ $pfx == 23andMe ]; then
    ns=98502
    nc=12588
    ne=36886.75
  else
    ns=98003
    nc=12455
    ne=36496.54
  fi
  zcat jamapsy_Giannakopoulou_2021_exclude_whi_$pfx.txt.gz | uniq | \
  sed 's/^\(rs142701510\t8\t2289342\t\)t\tc/\1a\tg/;s/^\(rs566706139\t8\t2289350\t\)t\tg/\1a\tc/;s/^\(rs74664568\t8\t2324610\t\)t\tc/\1a\tg/' | \
  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta \
    -s MDD_2021 --ns $ns --nc $nc --ne $ne | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o jamapsy_Giannakopoulou_2021_exclude_whi_$pfx.hg38.bcf -Ob --write-index
done

bcftools +pgs \
  --no-version \
  --beta-cov 3e-8 \
  --max-alpha-hat2 0.001 \
  --exclude 'FILTER="IFFY"' \
  jamapsy_Giannakopoulou_2021_exclude_whi_23andMe_ukb.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output jamapsy_Giannakopoulou_2021_exclude_whi_23andMe_ukb.hg38.pgs.b3e8.bcf \
  --output-type b \
  --log jamapsy_Giannakopoulou_2021_exclude_whi_23andMe_ukb.hg38.pgs.b3e8.log \
  --write-index

Tourette Syndrome

Download TS summary statistics frm 2019 TS study

wget -O TS_Oct2018.gz https://figshare.com/ndownloader/files/28169940

zcat TS_Oct2018.gz | sort -k2,2n -k3,3n | \
sed 's/^\(rs8075185 17 36060216 \)A G/\1T C/;s/^\(rs2855958 7 142170167 \)T C/\1A G/;s/^\(rs17274 7 142224511 \)T C/\1A G/' | \
bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s TS_2019 --ns 14307 --nc 4819 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o TS_Oct2018.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 2e-7 \
  --max-alpha-hat2 0.002 \
  --exclude 'FILTER="IFFY"' \
  TS_Oct2018.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output TS_Oct2018.hg38.pgs.b2e-7.bcf \
  --output-type b \
  --log TS_Oct2018.hg38.pgs.b2e-7.log \
  --write-index

Obsessive compulsive disorder

Download OCD summary statistics from 2018 OCD study

wget -O ocd_aug2017.gz https://figshare.com/ndownloader/files/28169544

bcftools +munge --no-version -Ou -c PLINK -f human_g1k_v37.fasta -s OCD_2018 ocd_aug2017.gz --ns 9725 --nc 2688 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o ocd_aug2017.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 2e-7 \
  --max-alpha-hat2 0.003 \
  --exclude 'FILTER="IFFY"' \
  ocd_aug2017.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output ocd_aug2017.hg38.pgs.b2e-7.bcf \
  --output-type b \
  --log ocd_aug2017.hg38.pgs.b2e-7.log \
  --write-index

Hoarding symptoms

Download hoarding summary statistics from 2022 hoarding study

wget -O hoarding2022.vcf.tsv.gz https://figshare.com/ndownloader/files/39399566

zcat hoarding2022.vcf.tsv.gz | grep -v ^$ | \
bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s hoarding_2022 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o hoarding2022.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 4e-8 \
  --max-alpha-hat2 0.001 \
  --exclude 'FILTER="IFFY"' \
  hoarding2022.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output hoarding2022.hg38.pgs.b4e-8.bcf \
  --output-type b \
  --log hoarding2022.hg38.pgs.b4e-8.log \
  --write-index

Post Traumatic Stress Disorder

Download PTSD summary statistics from 2019 PTSD study

wget -O pts_all_freeze2_overall.results.gz https://figshare.com/ndownloader/files/28169634

bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta \
  -s PTSD_2019 pts_all_freeze2_overall.results.gz | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o pts_all_freeze2_overall.hg38.bcf -Ob --write-index

For ancestry specific results on the autosomes

wget -O pts_aam_freeze2_overall.results.gz https://figshare.com/ndownloader/files/28169712
wget -O pts_eur_freeze2_overall.results.gz https://figshare.com/ndownloader/files/28169727
wget -O pts_lat_freeze2_overall.results.gz https://figshare.com/ndownloader/files/28169733

echo -e "AFR aam\nEUR eur\nAMR lat" | \
while read anc type; do
  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta \
    -s PTSD_2019.$anc pts_${type}_freeze2_overall.results.gz | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o pts_${type}_freeze2_overall.hg38.bcf -Ob --write-index
done
bcftools merge --no-version -m none -o pts_freeze2_overall.hg38.bcf -Ob \
  pts_{aam,eur,lat}_freeze2_overall.hg38.bcf --write-index
/bin/rm pts_{aam,eur,lat}_freeze2_overall.hg38.bcf

bcftools +pgs \
  --no-version \
  --beta-cov 4e-8 \
  --max-alpha-hat2 0.001 \
  --samples PTSD_2019.AFR,PTSD_2019.EUR,PTSD_2019.AMR \
  pts_freeze2_overall.hg38.bcf \
  1kg_ldgm.{AFR,EUR,AMR}.bcf \
  --output pts_freeze2_overall.hg38.pgsx.b4e-8.bcf \
  --output-type b \
  --log pts_freeze2_overall.hg38.pgsx.b4e-8.log \
  --write-index

Schizophrenia

Download SCZ summary statistics from 2022 SCZ study

wget -O PGC3_SCZ_wave3.primary.autosome.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517861
wget -O PGC3_SCZ_wave3.primary.chrX.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517864
wget -O PGC3_SCZ_wave3.core.autosome.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517807
wget -O PGC3_SCZ_wave3.core.chrX.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517825

for type in primary core; do
  for pfx in autosome chrX; do
    zcat PGC3_SCZ_wave3.$type.$pfx.public.v3.vcf.tsv.gz | sed 's/NEFF$/NEFFDIV2/;/\t$/d' | \
    bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s SCZ_2022.$type | \
    bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
      -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
    bcftools sort -o PGC3_SCZ_wave3.$type.$pfx.public.v3.hg38.bcf -Ob --write-index
  done
  bcftools concat --no-version --allow-overlaps -o PGC3_SCZ_wave3.$type.public.v3.hg38.bcf -Ob \
    PGC3_SCZ_wave3.$type.{autosome,chrX}.public.v3.hg38.bcf --write-index
  /bin/rm PGC3_SCZ_wave3.$type.{autosome,chrX}.public.v3.hg38.bcf{,.csi}
done

For ancestry specific results on the autosomes

wget -O PGC3_SCZ_wave3.afram.autosome.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517801
wget -O PGC3_SCZ_wave3.asian.autosome.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517804
wget -O PGC3_SCZ_wave3.european.autosome.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517828
wget -O PGC3_SCZ_wave3.latino.autosome.public.v3.vcf.tsv.gz https://figshare.com/ndownloader/files/34517855

echo -e "AFR afram\nEAS asian\nEUR european\nAMR latino" | \
while read anc type; do
  if [ type=="afram" ]; then opt="--ns 9824 --nc 5998 --ne 9234.7"; else opt=""; fi
  if [ type=="latino" ]; then opt="--ns 4324 --nc 1234 --ne 3335.2"; else opt=""; fi
  zcat PGC3_SCZ_wave3.$type.autosome.public.v3.vcf.tsv.gz | sed 's/NEFF$/NEFFDIV2/' | \
  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s SCZ_2022.$anc $opt | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o PGC3_SCZ_wave3.$type.autosome.public.v3.hg38.bcf -Ob --write-index
done
bcftools merge --no-version -m none -o PGC3_SCZ_wave3.autosome.public.v3.hg38.bcf -Ob \
  PGC3_SCZ_wave3.{afram,asian,european,latino}.autosome.public.v3.hg38.bcf --write-index
/bin/rm PGC3_SCZ_wave3.{afram,asian,european,latino}.autosome.public.v3.hg38.bcf{,.csi}

bcftools +pgs \
  --no-version \
  --beta-cov 2e-7 \
  --max-alpha-hat2 0.002 \
  --samples SCZ_2022.AFR,SCZ_2022.EAS,SCZ_2022.EUR,SCZ_2022.AMR \
  --exclude 'FILTER="IFFY"' \
  PGC3_SCZ_wave3.autosome.public.v3.hg38.bcf \
  1kg_ldgm.{AFR,EAS,EUR,AMR}.bcf \
  --output PGC3_SCZ_wave3.autosome.public.v3.hg38.pgsx.b2e-7.bcf \
  --output-type b \
  --log PGC3_SCZ_wave3.autosome.public.v3.hg38.pgsx.b2e-7.log \
  --write-index

Suicide

Download SUI summary statistics from 2022 SUI study (notice that you will need a Dropbox link provided from PGC.DAC.SUI)

wget -O daner_model2_062620_eur.neff.qc2.80.gz "https://www.dropbox.com/sh/<ISGC2021_D>/<ISGC2021_ID>_<ISGC2021_ID>/daner_model2_062620_eur.neff.qc2.80.gz?dl=0"

zcat daner_model2_062620_eur.neff.qc2.80.gz | sed 's/\.y\t/\t/g' | \
bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s SUI_2022 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o daner_model2_062620_eur.neff.qc2.80.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 1e-7 \
  --max-alpha-hat2 0.0005 \
  --exclude 'FILTER="IFFY"' \
  daner_model2_062620_eur.neff.qc2.80.bcf \
  1kg_ldgm.EUR.bcf \
  --output daner_model2_062620_eur.neff.qc2.80.pgs.b1e7.bcf \
  --output-type b \
  --log daner_model2_062620_eur.neff.qc2.80.pgs.b1e7.log \
  --write-index

Educational Attainment

Download EDU summary statistics from 2022 EDU study

wget https://ssgac.s3.amazonaws.com/ReadMe_EA4.txt
wget https://ssgac.s3.amazonaws.com/EA4_additive_p1e-5_clumped.txt
wget https://ssgac.s3.amazonaws.com/EA4_chrX_p1e-5_clumped.txt

for pfx in additive chrX; do
  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s EA_2022 EA4_${pfx}_p1e-5_clumped.txt | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o EA4_${pfx}_p1e-5_clumped.hg38.bcf -Ob --write-index
done
bcftools concat --no-version --allow-overlaps -o EA4_p1e-5_clumped.hg38.bcf -Ob \
  EA4_{additive,chrX}_p1e-5_clumped.hg38.bcf --write-index
/bin/rm EA4_{additive,chrX}_p1e-5_clumped.hg38.bcf{,.csi}

Intelligence

Download IQ summary statistics from 2018 IQ study

wget https://ctg.cncr.nl/documents/p1651/SavageJansen_IntMeta_sumstats.zip

unzip -p SavageJansen_IntMeta_sumstats.zip sumstats/SavageJansen_2018_intelligence_metaanalysis.txt | \
bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s IQ_2018 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o SavageJansen_IntMeta.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 1e-7 \
  --max-alpha-hat2 0.0005 \
  --exclude 'FILTER="IFFY"' \
  SavageJansen_IntMeta.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output SavageJansen_IntMeta.hg38.pgs.b1e7.bcf \
  --output-type b \
  --log SavageJansen_IntMeta.hg38.pgs.b1e7.log \
  --write-index

Height

Download Height summary statistics from 2022 Height study

wget https://cnsgenomics.com/data/giant_2022/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL.gz

bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta \
  -s HEIGHT_2022 GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL.gz | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL.hg38.bcf -Ob --write-index

For ancestry specific results on the autosomes

wget https://cnsgenomics.com/data/giant_2022/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_AFR.gz
wget https://cnsgenomics.com/data/giant_2022/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_EAS.gz
wget https://cnsgenomics.com/data/giant_2022/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_EUR.gz
wget https://cnsgenomics.com/data/giant_2022/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_HIS.gz
wget https://cnsgenomics.com/data/giant_2022/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_SAS.gz

echo -e "AFR AFR\nEAS EAS\nEUR EUR\nAMR HIS\nSAS SAS" | \
while read anc type; do
  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s HEIGHT_2022.$anc \
    GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_$type.gz | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_$type.hg38.bcf -Ob --write-index
done
bcftools merge --no-version -m none -o GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS.hg38.bcf -Ob \
  GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_{AFR,EAS,EUR,HIS,SAS}.hg38.bcf --write-index
/bin/rm GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_{AFR,EAS,EUR,HIS,SAS}.hg38.bcf

bcftools +pgs \
  --no-version \
  --beta-cov 1e-7 \
  --max-alpha-hat2 0.005 \
  --samples HEIGHT_2022.AFR,HEIGHT_2022.EAS,HEIGHT_2022.EUR,HEIGHT_2022.AMR,HEIGHT_2022.SAS \
  GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS.hg38.bcf \
  1kg_ldgm.{AFR,EAS,EUR,AMR,SAS}.bcf \
  --output GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS.hg38.pgsx.b1e-7.bcf \
  --output-type b \
  --log GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS.hg38.pgsx.b1e-7.log \
  --write-index

BMI

Download BMI summary statistics from 2018 BMI study

wget https://portals.broadinstitute.org/collaboration/giant/images/c/c8/Meta-analysis_Locke_et_al%2BUKBiobank_2018_UPDATED.txt.gz

bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta \
  -s BMI_2018 Meta-analysis_Locke_et_al+UKBiobank_2018_UPDATED.txt.gz | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o Meta-analysis_Locke_et_al+UKBiobank_2018_UPDATED.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 2e-7 \
  --max-alpha-hat2 0.002 \
  Meta-analysis_Locke_et_al+UKBiobank_2018_UPDATED.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output Meta-analysis_Locke_et_al+UKBiobank_2018_UPDATED.hg38.pgs.b2e-7.bcf \
  --output-type b \
  --log Meta-analysis_Locke_et_al+UKBiobank_2018_UPDATED.hg38.pgs.b2e-7.log \
  --write-index

Smoking

Download Smoking summary statistics from 2019 Smoking study

wget https://conservancy.umn.edu/bitstream/handle/11299/201564/SmokingInitiation.txt.gz

bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s SMOKING_2019 SmokingInitiation.txt.gz | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o SmokingInitiation.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 2e-8 \
  --max-alpha-hat2 0.0005 \
  SmokingInitiation.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output SmokingInitiation.hg38.pgs.b2e-8.bcf \
  --output-type b \
  --log SmokingInitiation.hg38.pgs.b2e-8.log \
  --write-index

Alzheimer

Download Alzheimer summary statistics from 2019 Alzheimer study

wget -O Kunkle_etal_Stage2_results.txt https://www.niagads.org/system/tdf/public_docs/Kunkle_etal_Stage2_results.txt?file=1

bcftools +munge --no-version -Ou \
  -C colheaders.tsv -f human_g1k_v37.fasta \
  -s AD_2019 Kunkle_etal_Stage2_results.txt | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o Kunkle_etal_Stage2_results.hg38.bcf -Ob --write-index

Download Alzheimer summary statistics from 2022 Alzheimer study

wget http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90027001-GCST90028000/GCST90027158/GCST90027158_buildGRCh38.tsv.gz

bcftools +munge --no-version -o GCST90027158.hg38.bcf -Ob -C colheaders.tsv \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
  -s AD_2022 GCST90027158_buildGRCh38.tsv.gz \
  --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 2e-8 \
  --max-alpha-hat2 0.002 \
  GCST90027158.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --exclude 'FILTER="IFFY"' \
  --output GCST90027158.hg38.pgs.b2e-8.bcf \
  --output-type b \
  --log GCST90027158.hg38.pgs.b2e-8.log \
  --write-index

bcftools +pgs \
  --no-version \
  --alpha-param 0 \
  --beta-cov 4e-8 \
  --max-alpha-hat2 0.002 \
  GCST90027158.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --exclude 'FILTER="IFFY"' \
  --output GCST90027158.hg38.pgs.a0.b4e-8.bcf \
  --output-type b \
  --log GCST90027158.hg38.pgs.a0.b4e-8.log \
  --write-index

Intracranial Volume

Download ICV summary statistics from 2016 ICV study

wget https://enigma.ini.usc.edu/wp-content/uploads/E2_C/CHARGE-ENIGMA-ICV-METAANALYSIS-201311141.TBL.FINAL.gz

zcat CHARGE-ENIGMA-ICV-METAANALYSIS-201311141.TBL.FINAL.gz | \
sed 's/^MarkerName/chromosome\tbase_pair_location/;s/:/\t/;/R\t/d;s/ /\t/g' | \
bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s ICV_2016 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o CHARGE-ENIGMA-ICV-METAANALYSIS-201311141.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 1e-7 \
  --max-alpha-hat2 0.005 \
  CHARGE-ENIGMA-ICV-METAANALYSIS-201311141.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output CHARGE-ENIGMA-ICV-METAANALYSIS-201311141.hg38.pgs.b1e-7.bcf \
  --output-type b \
  --log CHARGE-ENIGMA-ICV-METAANALYSIS-201311141.hg38.pgs.b1e-7.log \
  --write-index

Hippocampal Volume

Download HV summary statistics from 2017 HV study

wget https://enigma.ini.usc.edu/wp-content/uploads/E2_C/CHARGE-ENIGMA-HV-METAANALYSIS-201311141.TBL.FINAL.gz

zcat CHARGE-ENIGMA-HV-METAANALYSIS-201311141.TBL.FINAL.gz | \
sed 's/^MarkerName/chromosome\tbase_pair_location/;s/:/\t/;/R\t/d;s/ /\t/g' | \
bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s HV_2017 | \
bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
  -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
bcftools sort -o CHARGE-ENIGMA-HV-METAANALYSIS-201311141.hg38.bcf -Ob --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 8e-8 \
  --max-alpha-hat2 0.004 \
  CHARGE-ENIGMA-HV-METAANALYSIS-201311141.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output CHARGE-ENIGMA-HV-METAANALYSIS-201311141.hg38.pgs.b8e-8.bcf \
  --output-type b \
  --log CHARGE-ENIGMA-HV-METAANALYSIS-201311141.hg38.pgs.b8e-8.log \
  --write-index

Cortical

Download Cortical summary statistics from 2020 Cereb. Cortex study

for pfx in SurfArea Thickness; do
  wget https://enigma.ini.usc.edu/downloads/ENIGMA3_Global/ENIGMA3_mixed_se_wo_Mean_Full_${pfx}_20190429.txt.gz

  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s ${pfx}_2020 \
    ENIGMA3_mixed_se_wo_Mean_Full_${pfx}_20190429.txt.gz | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o ENIGMA3_mixed_se_wo_Mean_Full_${pfx}_20190429.hg38.bcf -Ob --write-index
done

bcftools +pgs \
  --no-version \
  --beta-cov 1e-7 \
  --max-alpha-hat2 0.005 \
  ENIGMA3_mixed_se_wo_Mean_Full_SurfArea_20190429.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output ENIGMA3_mixed_se_wo_Mean_Full_SurfArea_20190429.hg38.pgs.b1e-7.bcf \
  --output-type b \
  --log ENIGMA3_mixed_se_wo_Mean_Full_SurfArea_20190429.hg38.pgs.b1e-7.log \
  --write-index

bcftools +pgs \
  --no-version \
  --beta-cov 4e-8 \
  --max-alpha-hat2 0.002 \
  ENIGMA3_mixed_se_wo_Mean_Full_Thickness_20190429.hg38.bcf \
  1kg_ldgm.EUR.bcf \
  --output ENIGMA3_mixed_se_wo_Mean_Full_Thickness_20190429.hg38.pgs.b4e-8.bcf \
  --output-type b \
  --log ENIGMA3_mixed_se_wo_Mean_Full_Thickness_20190429.hg38.pgs.b4e-8.log \
  --write-index

Oscillatory Brain Activity

Download EEG summary statistics from 2018 EEG study

echo alphaCz alphaOcc betaCz deltaCz peakOcc thetaCz | tr ' ' '\n' | cat -n | \
while read n pfx; do
  wget -O ENIGMA-EEG_20181101_$pfx.txt.gz 'https://enigma-brain.org/download/sumstats/getFiles.php?key=MmIyZTNmMzljNWRiYWM0OWY2OTAwZGFlNjUxMTNmZTM=&f='$n

  bcftools +munge --no-version -Ou -C colheaders.tsv -f human_g1k_v37.fasta -s ${pfx}_2018 \
    ENIGMA-EEG_20181101_$pfx.txt.gz | \
  bcftools +liftover --no-version -Ou -- -s human_g1k_v37.fasta \
    -f GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -c hg19ToHg38.over.chain.gz | \
  bcftools sort -o ENIGMA-EEG_20181101_$pfx.hg38.bcf -Ob --write-index
done

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examples.md

examples.md

Polygenic score examples

Examples

Attention Deficit Hyperactivity Disorder

Anxiety Disorder

Autism Spectrum Disorder

Bipolar Disorder

Anorexia Nervosa

Major Depressive Disorder

Tourette Syndrome

Obsessive compulsive disorder

Hoarding symptoms

Post Traumatic Stress Disorder

Schizophrenia

Suicide

Educational Attainment

Intelligence

Height

BMI

Smoking

Alzheimer

Intracranial Volume

Hippocampal Volume

Cortical

Oscillatory Brain Activity

Files

examples.md

Latest commit

History

examples.md

File metadata and controls

Polygenic score examples

Examples

Attention Deficit Hyperactivity Disorder

Anxiety Disorder

Autism Spectrum Disorder

Bipolar Disorder

Anorexia Nervosa

Major Depressive Disorder

Tourette Syndrome

Obsessive compulsive disorder

Hoarding symptoms

Post Traumatic Stress Disorder

Schizophrenia

Suicide

Educational Attainment

Intelligence

Height

BMI

Smoking

Alzheimer

Intracranial Volume

Hippocampal Volume

Cortical

Oscillatory Brain Activity