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Commit a2d0dca9 authored by Brandi Cantarel's avatar Brandi Cantarel
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more nodes strelka

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variants/germline_vc.sh
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......@@ -124,8 +124,8 @@ then
gvcflist="$gvcflist --bam ${i}"
done
configManta.py $gvcflist --referenceFasta ${reffa} $mode --runDir manta
manta/runWorkflow.py -m local -j 8
manta/runWorkflow.py -m local -j $SLURM_CPUS_ON_NODE
configureStrelkaGermlineWorkflow.py $gvcflist --referenceFasta ${reffa} $mode --indelCandidates manta/results/variants/candidateSmallIndels.vcf.gz --runDir strelka
strelka/runWorkflow.py -m local -j 8
strelka/runWorkflow.py -m local -j $SLURM_CPUS_ON_NODE
bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.strelka2.vcf.gz strelka/results/variants/variants.vcf.gz
fi
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