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Verified Commit df5c19a1 authored by Laurent Modolo's avatar Laurent Modolo
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gatk3: fix high_confidence_snp_filter call

parent c8c10187
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......@@ -97,8 +97,8 @@ gatk3 -T SelectVariants \
"""
}
high_confidence_snp_filter = "(QD < 2.0) || (FS > 60.0) || (MQ < 40.0) || (MQRankSum < -12.5) || (ReadPosRankSum < -8.0) || (SOR > 4.0)"
params.high_confidence_snp = "--filterExpression \"${high_confidence_snp_filter}\" --filterName \"basic_snp_filter\""
params.high_confidence_snp_filter = "(QD < 2.0) || (FS > 60.0) || (MQ < 40.0) || (MQRankSum < -12.5) || (ReadPosRankSum < -8.0) || (SOR > 4.0)"
params.high_confidence_snp = "--filterExpression \"${params.high_confidence_snp_filter}\" --filterName \"basic_snp_filter\""
params.high_confidence_snp_out = ""
process high_confidence_snp {
container = "${container_url}"
......@@ -129,8 +129,8 @@ gatk3 -T VariantFiltration \
"""
}
high_confidence_indel_filter = "QD < 3.0 || FS > 200.0 || ReadPosRankSum < -20.0 || SOR > 10.0"
params.high_confidence_indels = "--filterExpression \"${high_confidence_indel_filter}\" --filterName \"basic_indel_filter\""
params.high_confidence_indel_filter = "QD < 3.0 || FS > 200.0 || ReadPosRankSum < -20.0 || SOR > 10.0"
params.high_confidence_indels = "--filterExpression \"${params.high_confidence_indel_filter}\" --filterName \"basic_indel_filter\""
params.high_confidence_indels_out = ""
process high_confidence_indels {
container = "${container_url}"
......
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