bugfix

README.md

@@ -16,6 +16,7 @@ Nat Genet. doi:10.1038/ng.3367.
 2. `wget` (pre-installed or via distribution package manager)
 3. `singularity` container software (tested on 3.3.0, https://sylabs.io/guides/3.3/user-guide)
 4. `git` (https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
+5. for data download fimm GCP bucket access to `fimm-horizon-outgoing-data/CENTER_TBI_data_freeze_190829/Imputed_data`
 
 ### Optional
 
@@ -39,6 +40,15 @@ Download the container image
 
     bash scripts/download_container.sh
 
+Obtain the imputed genomes (GCP bucket: fimm-horizon-outgoing-data/CENTER_TBI_data_freeze_190829/Imputed_data).
+`gsutils` is pre-installed in the container image, to authenticate with your
+GCP account run and follow the interactive instructions
+
+    singularity shell container.sif
+    gcloud auth login
+    snakemake download_imputed_genotypes
+    exit
+
 Execute the workflow inside the container on a single core (takes a while!)
 
     singularity exec container.sif snakemake impute

Snakefile

@@ -70,7 +70,7 @@ rule vcf_to_dosages:
         export prefix={wildcards.output_dir}/dosages
         mkdir -p $prefix
         echo "extracting and computing MAFs ..."
-        bcftools +fill-tags {inputs.vcf_gz_file} > $prefix/chr{wildcards.i}.vcf
+        bcftools +fill-tags {input.vcf_gz_file} > $prefix/chr{wildcards.i}.vcf
         echo 'querying dosages ...'
         bcftools query -e 'MAF[0]>{config[min_MAF]} | INFO>{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' -f '%CHROM %ID %POS %REF %ALT %INFO/MAF [%DS ]\n' $prefix/chr{wildcards.i}.vcf > $prefix/chr{wildcards.i}.dosage.txt
         echo 'compressing ...'
@@ -94,7 +94,7 @@ rule generate_samples_file:
         """
         export prefix={wildcards.output_dir}/dosages
         mkdir -p $prefix
-        bcftools query -l {inputs.vcf_gz_file} >> $prefix/samples_.txt
+        bcftools query -l {input.vcf_gz_file} >> $prefix/samples_.txt
         # family ID = individual ID
         awk {params.format} < $prefix/samples_.txt > $prefix/samples.txt
         rm $prefix/samples_.txt