Sort vcf after SVConcordance

broadinstitute · Dec 14, 2023 · 4881329 · 4881329
1 parent 7607a32
commit 4881329
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Showing 2 changed files with 8 additions and 3 deletions.
diff --git a/inputs/values/dockers.json b/inputs/values/dockers.json
@@ -2,7 +2,7 @@
   "name": "dockers",
   "cnmops_docker": "us.gcr.io/broad-dsde-methods/gatk-sv/cnmops:2023-07-28-v0.28.1-beta-e70dfbd7",
   "condense_counts_docker": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
-  "gatk_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:2023-07-13-4.4.0.0-43-gd79823f9c-NIGHTLY-SNAPSHOT",
+  "gatk_docker": "us.gcr.io/broad-dsde-methods/markw/gatk:mw-sv-concordance-opt-1097258",
   "gatk_docker_pesr_override": "us.gcr.io/broad-dsde-methods/tsharpe/gatk:4.2.6.1-57-g9e03432",
   "genomes_in_the_cloud_docker": "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.2-1510681135",
   "linux_docker": "marketplace.gcr.io/google/ubuntu1804",

diff --git a/wdl/SVConcordance.wdl b/wdl/SVConcordance.wdl
@@ -81,7 +81,7 @@ task SVConcordanceTask {
   RuntimeAttr default_attr = object {
                                cpu_cores: 1,
                                mem_gb: 16,
-                               disk_gb: ceil(10 + size(eval_vcf, "GB") * 2 + size(truth_vcf, "GB")),
+                               disk_gb: ceil(10 + size(eval_vcf, "GB") * 4 + size(truth_vcf, "GB")),
                                boot_disk_gb: 10,
                                preemptible_tries: 3,
                                max_retries: 1
@@ -113,8 +113,13 @@ task SVConcordanceTask {
       --sequence-dictionary ~{reference_dict} \
       --eval ~{eval_vcf} \
       --truth ~{truth_vcf} \
-      -O ~{output_prefix}.vcf.gz \
+      -O unsorted.vcf.gz \
+      --do-not-sort \
       ~{additional_args}
+
+    mkdir tmp
+    bcftools sort --max-mem ${JVM_MAX_MEM}M -T tmp -Oz -o ~{output_prefix}.vcf.gz unsorted.vcf.gz
+    tabix ~{output_prefix}.vcf.gz
   >>>
   runtime {
     cpu: select_first([runtime_attr.cpu_cores, default_attr.cpu_cores])