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Verified Commit 93c9b2e9 authored by Laurent Modolo's avatar Laurent Modolo
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gatk4: fix SelectVariants cmd (remove -T)

parent b18b1efe
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......@@ -56,7 +56,7 @@ process filter_indels {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G"-T SelectVariants \
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
-R ${fasta} \
-V ${vcf} \
-selectType INDEL \
......@@ -79,7 +79,7 @@ process high_confidence_snp {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G"-T VariantFiltration \
gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
-R ${fasta} \
-V ${vcf} \
--filterExpression "${high_confidence_snp_filter}" \
......
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