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run-vcf2flat.sh
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executable file
·42 lines (39 loc) · 2.48 KB
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#!/bin/bash
input_file="\
/flush/obr17q/phase3/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr2.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr3.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr4.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr5.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr7.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr8.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr9.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr10.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr11.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr12.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr13.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr14.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr15.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr16.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr17.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr18.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr19.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr20.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr21.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf,\
/flush/obr17q/phase3/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf\
"
clusters=5
IncludeGroups=""
ExcludeGroups=""
VariantCutoff="0"
spark-submit --class au.csiro.obr17q.variantspark.VcfToFlatVariant \
--master yarn-client \
--num-executors 200 \
--executor-memory 4G \
--executor-cores 1 \
--driver-memory 4G \
variantspark/target/variantspark-0.0.1-SNAPSHOT.jar \
$input_file \
/flush2/szu004/variant/phase3.flat.parquet \
$VariantCutoff