psychimmgenA13.Rmd

---
title: "Process ASD SSs and do s-LDSC"
output: html_notebook
editor_options: 
  chunk_output_type: console
---

Asd_grove2017
iPSYCH-PGC_ASD_Nov2017.gz: Full ASD GWAS meta-analysis of samples of European ancestry
(18,382 cases, 27,969 controls)

Munge sumstats
```{bash}

LDSCDIR=/Users/mary/non_dropbox/exps/ldsc
cd $LDSCDIR
FORLDSCDIR=~/Library/Mobile\ Documents/com~apple~CloudDocs/Documents/research/exps/forldsc

deactivate
conda activate ldsc

${LDSCDIR}/munge_sumstats.py --sumstats /Users/mary/Documents/research/exps/summary_stats/asd/iPSYCH-PGC_ASD_Nov2017 --N-cas 18382 --N-con 27969 --signed-sumstats OR,1 --merge-alleles ${FORLDSCDIR}/w_hm3.snplist --out asd_grove --snp SNP --chunksize 500000 --a1 A1 --a2 A2 --p P --info INFO 

```

s-LDSC
```{bash}

cd $LDSCDIR
cts_name=IDEASv1_active

# Ensure we are using original rather than conditional models
cp $LDSCDIR/${cts_name}_original.ldcts $LDSCDIR/$cts_name.ldcts

python ${LDSCDIR}/ldsc.py --h2-cts $LDSCDIR/asd_grove.sumstats.gz --ref-ld-chr ${LDSCDIR}/baseline_v1.2/baseline. --out asd_grove_cts_${cts_name} --ref-ld-chr-cts $LDSCDIR/$cts_name.ldcts --w-ld-chr ${LDSCDIR}/1000G_Phase3_weights_hm3_no_MHC/weights.hm3_noMHC. 

```