diff --git a/CollectSamError/CollectSamErrorMetrics.wdl b/CollectSamError/CollectSamErrorMetrics.wdl index e1353e0..82fb7de 100644 --- a/CollectSamError/CollectSamErrorMetrics.wdl +++ b/CollectSamError/CollectSamErrorMetrics.wdl @@ -44,11 +44,12 @@ task CollectSamErrorMetricsTask { Int disk_gb = 400 Int memory_gb = 16 Int minMQ = 60 + Float probability = 1.0 } command { java -Xms2000m -jar /usr/gitc/picard.jar CollectSamErrorMetrics I=~{input_bam} \ - O=~{output_name} R=~{ref_fasta} V=~{vcf_file} L=~{intervals} MQ=~{minMQ} \ + O=~{output_name} R=~{ref_fasta} V=~{vcf_file} L=~{intervals} MQ=~{minMQ} P=~{probability} \ ERROR_METRICS=null \ ERROR_METRICS="ERROR:INSERT_LENGTH" \ ERROR_METRICS="ERROR:CYCLE" \ @@ -56,7 +57,9 @@ task CollectSamErrorMetricsTask { ERROR_METRICS="ERROR:BASE_QUALITY" \ ERROR_METRICS="ERROR:ONE_BASE_PADDED_CONTEXT" \ ERROR_METRICS="ERROR:HOMOPOLYMER" \ + ERROR_METRICS="OVERLAPPING_ERROR:INSERT_LENGTH" \ ERROR_METRICS="OVERLAPPING_ERROR:CYCLE" \ + ERROR_METRICS="OVERLAPPING_ERROR:GC_CONTENT" \ ERROR_METRICS="OVERLAPPING_ERROR:BASE_QUALITY" \ ERROR_METRICS="OVERLAPPING_ERROR:ONE_BASE_PADDED_CONTEXT" \ ERROR_METRICS="OVERLAPPING_ERROR:HOMOPOLYMER"