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Merge pull request #37 from MRCIEU/revert_fastgwa
Revert fastgwa
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| #!/bin/bash | ||
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| # strict stop if there are any errors | ||
| set -e | ||
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| # get environmental variables | ||
| source config.env | ||
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| # create results directory | ||
| mkdir -p ${results_dir}/00 | ||
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| # log everything from this script to a logfile in the results directory | ||
| exec &> >(tee ${results_dir}/00/logfile) | ||
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| echo "Get MAF and INFO scores" | ||
| Rscript resources/genotypes/rand.r ${genotype_processed_dir}/sample_inclusion.txt ${genotype_processed_dir}/scratch/phenrand.txt | ||
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| samplefile=$(head -n 1 ${genotype_input_list} | awk '{print $2}') | ||
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| ./bin/gcta-1.94.1 \ | ||
| --mbgen ${genotype_input_list} \ | ||
| --sample ${samplefile} \ | ||
| --pheno ${genotype_processed_dir}/scratch/phenrand.txt \ | ||
| --fastGWA-lr \ | ||
| --keep ${genotype_processed_dir}/sample_inclusion.txt \ | ||
| --thread-num ${env_threads} \ | ||
| --maf 0 \ | ||
| --geno 1 \ | ||
| --out ${genotype_processed_dir}/scratch/phenrand | ||
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| Rscript resources/genotypes/organise_variants.r \ | ||
| ${genotype_processed_dir}/scratch/phenrand.fastGWA \ | ||
| ${results_dir}/00 \ | ||
| ${genotype_processed_dir}/variant_inclusion.txt \ | ||
| ${genotype_processed_dir}/build_mapping.txt | ||
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| echo "Successfully summarised and filtered variants" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| #!/bin/bash | ||
|
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| # strict stop if there are any errors | ||
| set -e | ||
|
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| # get environmental variables | ||
| source config.env | ||
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| # create results directory | ||
| mkdir -p ${results_dir}/04 | ||
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| # log everything from this script to a logfile in the results director | ||
| exec &> >(tee ${results_dir}/04/logfile_step1) | ||
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| # Inputs: | ||
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| # - sparse GRM - 01 | ||
| # - PCs - 01 | ||
| # - genotype data - 00 | ||
| # - phenotypes - 02 | ||
| # - covariates - 00 | ||
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| # Processes: | ||
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| # - FastGWA per phen x age x ancestry | ||
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| # Output: | ||
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| # - GWAS summary stats per phen x age x ancestry | ||
| # - results/04/phen_<phencode>_<ancestry>_<age>.* | ||
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| phenolist=( $(cat ${phenotype_processed_dir}/phenolist) ) | ||
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| # Allow specific analysis to be run | ||
| # Can take any number between 1:ngwas where ngwas is the number of rows in ${phenotype_processed_dir}/phenolist | ||
| index=$1 | ||
| nphen=`cat ${phenotype_processed_dir}/phenolist | wc -l` | ||
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| if [ -z $index ] | ||
| then | ||
| echo "Running all $nphen GWASs" | ||
| elif [ ! -z $index ]; then | ||
| re='^[0-9]+$' | ||
| if ! [[ $index =~ $re ]] ; then | ||
| # check if $index is in the phenolist array | ||
| if [[ " ${phenolist[@]} " =~ " ${index} " ]]; then | ||
| echo "Running GWAS for phenotype $index" | ||
| else | ||
| echo "error: Index is not a number or a valid phenotype" | ||
| echo "Usage: ${0} [index number]" | ||
| exit 1 | ||
| fi | ||
| else | ||
| if [ "$index" -gt "$nphen" ] ; then | ||
| echo "error: Index is larger than number of phenotypes" | ||
| echo "Usage: ${0} [index number]" | ||
| exit 1 | ||
| fi | ||
| echo "Running $index of $nphen GWASs" | ||
| fi | ||
| fi | ||
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| echo $index | ||
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| ## TODO | ||
| # copy bim files over to results/04 | ||
| # Do GWAS for each phenotype | ||
| i=1 | ||
| samplefile=$(head -n 1 ${genotype_input_list} | awk '{print $2}') | ||
| for phen in ${phenolist[@]} | ||
| do | ||
| if [ -z $index ] || [[ "$index" == "$phen" ]] || [[ "$index" == "$i" ]] ; then | ||
| filename=$(basename -- ${phen}) | ||
| filename="${filename%.*}" | ||
| echo $filename | ||
| covs=$(echo $phen | sed 's/.phen$/.covs/1') | ||
| echo $covs | ||
| echo "0" > ${phen}.flag | ||
| if [ "$env_family_data" == "true" ] | ||
| then | ||
| echo "family" | ||
| ( | ||
| ./bin/gcta-1.94.1 \ | ||
| --mbgen ${genotype_input_list} \ | ||
| --sample ${samplefile} \ | ||
| --fastGWA-mlm \ | ||
| --grm-sparse ${genotype_processed_dir}/sparsegrm \ | ||
| --extract ${genotype_processed_dir}/variant_inclusion.txt \ | ||
| --keep ${genotype_processed_dir}/sample_inclusion.txt \ | ||
| --pheno ${phen} \ | ||
| --qcovar ${covs} \ | ||
| --thread-num ${env_threads} \ | ||
| --maf 0 \ | ||
| --geno 1 \ | ||
| --out ${results_dir}/04/${filename} | ||
| ) || ( echo "1" > ${phen}.flag ) | ||
| flag=`cat ${phen}.flag` | ||
| echo $flag | ||
| if [ "$flag" -eq "1" ] ; then | ||
| echo "LMM failed. Trying linear model using unrelateds only" | ||
| ./bin/gcta-1.94.1 \ | ||
| --mbgen ${genotype_input_list} \ | ||
| --sample ${samplefile} \ | ||
| --fastGWA-mlm \ | ||
| --grm-sparse ${genotype_processed_dir}/sparsegrm \ | ||
| --extract ${genotype_processed_dir}/variant_inclusion.txt \ | ||
| --keep ${genotype_processed_dir}/sample_inclusion.txt \ | ||
| --pheno ${phen} \ | ||
| --qcovar ${covs} \ | ||
| --thread-num ${env_threads} \ | ||
| --maf 0 \ | ||
| --geno 1 \ | ||
| --out ${results_dir}/04/${filename} | ||
| fi | ||
| else | ||
| echo "not family" | ||
| ./bin/gcta-1.94.1 \ | ||
| --mbgen ${genotype_input_list} \ | ||
| --sample ${samplefile} \ | ||
| --fastGWA-lr \ | ||
| --pheno ${phen} \ | ||
| --extract ${genotype_processed_dir}/variant_inclusion.txt \ | ||
| --keep ${genotype_processed_dir}/sample_inclusion.txt \ | ||
| --qcovar ${covs} \ | ||
| --thread-num ${env_threads} \ | ||
| --maf 0 \ | ||
| --geno 1 \ | ||
| --out ${results_dir}/04/${filename} | ||
| fi | ||
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| # compress GWAS | ||
| # keep only b, se because all other info is constant across GWASs | ||
| echo "Compressing output..." | ||
| Rscript resources/genotypes/compress_gwas.r ${results_dir}/04/${filename}.fastGWA ${genotype_processed_dir}/build_mapping.txt | ||
| rm ${results_dir}/04/${filename}.fastGWA | ||
| fi | ||
| i=$((i+1)) | ||
| done |
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