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impute-gene-expression
impute-gene-expression
Commit e797edd1 authored by Kevin Kunzmann's avatar Kevin Kunzmann
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earlier filtering

parent 18832746
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Showing with 3 additions and 3 deletions
Snakefile
View file @ e797edd1
...@@ -82,8 +82,6 @@ rule vcf_to_dosages: ...@@ -82,8 +82,6 @@ rule vcf_to_dosages:
printf "done.\n\r\n\r" 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 # extract sample file for PrediXcan
rule generate_samples_file: rule generate_samples_file:
input: input:
......
scripts/slurm-snakemake.sh
View file @ e797edd1
mkdir logs mkdir -p logs
rm -f nohup.out
touch nohup.out
nohup snakemake $1 \ nohup snakemake $1 \
--jobs 99 \ --jobs 99 \
--use-singularity \ --use-singularity \
......
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