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Plot SV counts at the end of the ClusterBatch module #389

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Plot SV counts at the end of the ClusterBatch module #389

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Plot SV counts at the end of ClusterBatch.
VJalili Aug 18, 2022
1947cfe
Update wdl/ClusterBatch.wdl
VJalili Aug 22, 2022
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4 changes: 3 additions & 1 deletion inputs/templates/test/ClusterBatch/ClusterBatch.json.tmpl
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Expand Up @@ -29,5 +29,7 @@
"ClusterBatch.wham_vcf_tar": {{ test_batch.std_wham_vcf_tar | tojson }},
"ClusterBatch.manta_vcf_tar": {{ test_batch.std_manta_vcf_tar | tojson }},
"ClusterBatch.melt_vcf_tar": {{ test_batch.std_melt_vcf_tar | tojson }},
"ClusterBatch.ped_file": {{ test_batch.ped_file | tojson }}
"ClusterBatch.ped_file": {{ test_batch.ped_file | tojson }},

"ClusterBatch.outlier_cutoff_nIQR": "10000"
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Suggested change
"ClusterBatch.outlier_cutoff_nIQR": "10000"
"ClusterBatch.outlier_cutoff_nIQR": "8"

10000 is used in FilterBatch to effectively disable sample filtering. Here we should make it something statistically reasonable, otherwise the cutoffs at +/- 10000 IQR make the plots unreadable.

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I've been using 6 for plotting

}
19 changes: 19 additions & 0 deletions wdl/ClusterBatch.wdl
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Expand Up @@ -5,6 +5,7 @@ import "DepthClustering.wdl" as depth
import "ClusterBatchMetrics.wdl" as metrics
import "TasksClusterBatch.wdl" as tasks
import "Utils.wdl" as util
import "PlotSVCountsPerSample.wdl" as sv_counts

workflow ClusterBatch {
input {
Expand Down Expand Up @@ -65,6 +66,8 @@ workflow ClusterBatch {

Float? java_mem_fraction

Int outlier_cutoff_nIQR
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I'd suggest making this an optional. If it's provided, we run PlotSVCountsPerSample. If not, it skips the task (we don't need to run this for the single sample pipeline for example). Would need to add this input and the outputs to GATKSVPipelinePhase1 and GATKSVPipelineBatch.


RuntimeAttr? runtime_attr_ids_from_vcf_list
RuntimeAttr? runtime_attr_create_ploidy
RuntimeAttr? runtime_attr_prepare_pesr_vcfs
Expand All @@ -82,6 +85,9 @@ workflow ClusterBatch {
RuntimeAttr? runtime_attr_gatk_to_svtk_vcf_depth
RuntimeAttr? runtime_override_concat_vcfs_depth
RuntimeAttr? runtime_attr_exclude_intervals_pesr
RuntimeAttr? runtime_attr_count_svs
RuntimeAttr? runtime_attr_plot_svcounts
RuntimeAttr? runtime_attr_cat_outliers_preview
}

call util.GetSampleIdsFromVcfTar {
Expand Down Expand Up @@ -282,9 +288,22 @@ workflow ClusterBatch {
}
}

call sv_counts.PlotSVCountsPerSample {
input:
prefix = batch,
vcfs = [select_first([ClusterPESR_manta.clustered_vcf]), select_first([ClusterPESR_wham.clustered_vcf]), select_first([ClusterPESR_melt.clustered_vcf]), select_first([ClusterPESR_scramble.clustered_vcf])],
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N_IQR_cutoff = outlier_cutoff_nIQR,
sv_pipeline_docker = sv_pipeline_docker,
runtime_attr_count_svs = runtime_attr_count_svs,
runtime_attr_plot_svcounts = runtime_attr_plot_svcounts,
runtime_attr_cat_outliers_preview = runtime_attr_cat_outliers_preview
}

output {
File clustered_depth_vcf = ClusterDepth.clustered_vcf
File clustered_depth_vcf_index = ClusterDepth.clustered_vcf_index
Array[File] sv_counts = PlotSVCountsPerSample.sv_counts
Array[File] sv_count_plots = PlotSVCountsPerSample.sv_count_plots
File? clustered_manta_vcf = ClusterPESR_manta.clustered_vcf
File? clustered_manta_vcf_index = ClusterPESR_manta.clustered_vcf_index
File? clustered_wham_vcf = ClusterPESR_wham.clustered_vcf
Expand Down