diff --git a/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md b/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md index 1447e70..ffcc10c 100644 --- a/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md +++ b/pipelines/EmpiricalMaps/EmpiricalMaps.changelog.md @@ -1,3 +1,9 @@ +# 1.3.1 + +* Make EmpiricalMaps for polyploids compatible with Reads2MapApp v0.0.2 +* Polyploid map quality diagnostic by resampling +* Adapt regenotyping memory usage + # 1.3.0 * Add MAPpoly new functions framework_map and update_framework_map @@ -7,7 +13,7 @@ # 1.2.5 -* more flexibility to choose the probability to be used in the HMM: +* more flexibility to choose the probability to be used in the HMM: * new parameters: - global_errors: array with global errors to be tested diff --git a/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md b/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md index cca2626..28c0d13 100644 --- a/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md +++ b/pipelines/EmpiricalSNPCalling/EmpiricalSNPCalling.changelog.md @@ -1,3 +1,9 @@ +# 1.4.4 + +* Make BarcodeFaker task work for input files that do not finish with .fasta or .fq +* Adapt BarcodeFaker required memory and time +* Adapt STACKs required memory + # 1.4.3 * Adapt tassel and stacks tasks also for polyploids @@ -32,7 +38,7 @@ # 1.2.0 * Run freebayes parallelizing in nodes according to chromosomes and cores splitting in genomic regions -* Adjust runtimes +* Adjust runtimes * Add polyploid dataset for tests # 1.1.0 diff --git a/tasks/gatk.wdl b/tasks/gatk.wdl index 5c879aa..4c8fe8c 100644 --- a/tasks/gatk.wdl +++ b/tasks/gatk.wdl @@ -299,7 +299,7 @@ task VariantFiltration { -filter "QUAL < 30.0" --filter-name "QUAL30" \ -filter "SOR > 3.0" --filter-name "SOR3" \ -filter "FS > 60.0" --filter-name "FS60" \ - -filter "MQ < 40.0" --filter-name "MQ50" \ + -filter "MQ < 40.0" --filter-name "MQ40" \ -filter "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" \ -filter "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum-8" \ -O gatk_filters.vcf.gz