earlier filtering

Snakefile

@@ -69,16 +69,21 @@ rule vcf_to_dosages:
         """
         export prefix={wildcards.output_dir}/dosages
         mkdir -p $prefix
-        echo "extracting and computing MAFs ..."
-        bcftools +fill-tags {input.vcf_gz_file} > $prefix/chr{wildcards.i}.vcf
+        echo "decompress and filter out: 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' ..."
+        bcftools filter -e 'MAF[0]<{config[min_MAF]} | INFO<{config[min_INFO]} | TYPE!="snp" | N_ALT!=1' > $prefix/chr{wildcards.i}_.vcf
+        echo "add computing MAFs ..."
+        bcftools $prefix/chr{wildcards.i}.vcf_ > $prefix/chr{wildcards.i}.vcf
+        rm $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
+        bcftools query -f '%CHROM %ID %POS %REF %ALT %INFO/MAF [%DS ]\n' $prefix/chr{wildcards.i}.vcf > $prefix/chr{wildcards.i}.dosage.txt
+        rm $prefix/chr{wildcards.i}.vcf
         echo 'compressing ...'
         gzip $prefix/chr{wildcards.i}.dosage.txt
-        rm $prefix/chr{wildcards.i}.vcf
         printf "done.\n\r\n\r"
         """
 
+bcftools +fill-tags -e 'MAF[0]<0.01 | INFO<0.8 | TYPE!="snp" | N_ALT!=1' CENTER_TBI_imputed_3695_1K_MAC1_freeze_190829_chr1.vcf.gz > chr1.vcf
+
 # extract sample file for PrediXcan
 rule generate_samples_file:
     input:

scripts/slurm-snakemake.sh

 mkdir logs
 nohup snakemake $1 \
-    --jobs 5 \
+    --jobs 99 \
     --use-singularity \
     --cluster-config cluster.json \
     --cluster "sbatch -A {cluster.account} -p {cluster.partition} --ntasks {cluster.ntasks} --cpus-per-task {cluster.ncpu} --nodes {cluster.nodes} -t {cluster.time} --job-name {cluster.name} --output {cluster.output} --error {cluster.error}" &