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CNV Tumor only WDL #4414

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merged 5 commits into from
Feb 15, 2018
Merged

CNV Tumor only WDL #4414

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54e7547
Tumor only WDL manually-tested and appears to be working. Still need…
LeeTL1220 Feb 8, 2018
a73619e
Added another test of tumor only.
LeeTL1220 Feb 13, 2018
df5aae3
Doc updates for the new WDL.
LeeTL1220 Feb 13, 2018
9f49927
Fixing coercion error
LeeTL1220 Feb 14, 2018
4839713
Answering PR comments.
LeeTL1220 Feb 14, 2018
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11 changes: 11 additions & 0 deletions scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wes_no-gc_tumor_only_workflow.json
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@@ -0,0 +1,11 @@
{
"CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list",
"CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__",
"CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/ice_targets_sample-chr20.interval_list",
"CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wes-no-gc.pon.hdf5",
"CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict",
"CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai",
"CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta",
"CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam",
"CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/SM-74P4M-v1-chr20-downsampled.deduplicated.bam.bai"
}
12 changes: 12 additions & 0 deletions scripts/cnv_cromwell_tests/somatic/cnv_somatic_pair_wgs_do-gc_tumor_only_workflow.json
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{
"CNVSomaticPairWorkflow.common_sites": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/common_snps_sample-chr20.interval_list",
"CNVSomaticPairWorkflow.gatk_docker": "__GATK_DOCKER__",
"CNVSomaticPairWorkflow.intervals": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/chr20.interval_list",
"CNVSomaticPairWorkflow.bin_length": "10000",
"CNVSomaticPairWorkflow.read_count_pon": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5",
"CNVSomaticPairWorkflow.ref_fasta_dict": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.dict",
"CNVSomaticPairWorkflow.ref_fasta_fai": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta.fai",
"CNVSomaticPairWorkflow.ref_fasta": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/human_g1k_v37.chr-20.truncated.fasta",
"CNVSomaticPairWorkflow.tumor_bam": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam",
"CNVSomaticPairWorkflow.tumor_bam_idx": "/home/travis/build/broadinstitute/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/HCC1143-t1-chr20-downsampled.deduplicated.bam.bai"
}
10 changes: 9 additions & 1 deletion scripts/cnv_cromwell_tests/somatic/run_cnv_somatic_workflows.sh
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Expand Up @@ -34,6 +34,8 @@ sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_T
sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_somatic_pair_wgs_no-gc_workflow.json >cnv_somatic_pair_wgs_no-gc_workflow_mod.json
sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_somatic_pair_wes_do-gc_workflow.json >cnv_somatic_pair_wes_do-gc_workflow_mod.json
sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_somatic_pair_wgs_do-gc_workflow.json >cnv_somatic_pair_wgs_do-gc_workflow_mod.json
sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_somatic_pair_wgs_do-gc_tumor_only_workflow.json > cnv_somatic_pair_wgs_do-gc_tumor_only_workflow_mod.json
sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" ${CNV_CROMWELL_TEST_DIR}/cnv_somatic_pair_wes_no-gc_tumor_only_workflow.json > cnv_somatic_pair_wes_no-gc_tumor_only_workflow_mod.json

echo "Running ========"
CROMWELL_JAR="cromwell-0.29.jar"
Expand All @@ -54,4 +56,10 @@ java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/c
# Pair WES w/ explicit GC correction
java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_do-gc_workflow_mod.json
# Pair WGS w/ explicit GC correction
java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_do-gc_workflow_mod.json
java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_do-gc_workflow_mod.json

# Tumor only WGS w/ explicit GC correction
java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wgs_do-gc_tumor_only_workflow_mod.json

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Remove white space to be consistent.

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Done

# Tumor only WES w/o explicit GC correction
java -jar ~/${CROMWELL_JAR} run /home/travis/build/broadinstitute/gatk/scripts/cnv_wdl/somatic/cnv_somatic_pair_workflow.wdl -i cnv_somatic_pair_wes_no-gc_tumor_only_workflow_mod.json
10 changes: 5 additions & 5 deletions scripts/cnv_wdl/somatic/README.md
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Expand Up @@ -24,10 +24,10 @@ The reference used must be the same between PoN and case samples.
- ``CNVSomaticPanelWorkflow.ref_fasta_fai`` -- Path to reference fasta fai file.
- ``CNVSomaticPanelWorkflow.ref_fasta`` -- Path to reference fasta file.

In additional, there are optional workflow-level and task-level parameters that may be set by advanced users; for example:
Additionally, there are optional workflow-level and task-level parameters that may be set by advanced users; for example:

- ``CNVSomaticPanelWorkflow.do_explicit_gc_correction`` -- (optional) If true, perform explicit GC-bias correction when creating PoN and in subsequent denoising of case samples. If false, rely on PCA-based denoising to correct for GC bias.
- ``CNVSomaticPanelWorkflow.PreprocessIntervals.bin_length`` -- Size of bins (in bp) for coverage collection. *This must be the same value used for all case samples.*
- ``CNVSomaticPanelWorkflow.PreprocessIntervals.bin_length`` -- Size of bins (in bp) for coverage collection. Typically, this is set to `0` for capture samples. *This must be the same value used for all case samples.*
- ``CNVSomaticPanelWorkflow.PreprocessIntervals.padding`` -- Amount of padding (in bp) to add to both sides of targets for WES coverage collection. *This must be the same value used for all case samples.*

Further explanation of other task-level parameters may be found by invoking the ``--help`` documentation available in the gatk.jar for each tool.
Expand All @@ -39,16 +39,16 @@ The reference and bins (if specified) must be the same between PoN and case samp
- ``CNVSomaticPairWorkflow.common_sites`` -- Picard or GATK-style interval list of common sites to use for collecting allelic counts.
- ``CNVSomaticPairWorkflow.gatk_docker`` -- GATK Docker image (e.g., ``broadinstitute/gatk:latest``).
- ``CNVSomaticPairWorkflow.intervals`` -- Picard or GATK-style interval list. For WGS, this should typically only include the autosomal chromosomes.
- ``CNVSomaticPairWorkflow.normal_bam`` -- Path to normal BAM file.
- ``CNVSomaticPairWorkflow.normal_bam_idx`` -- Path to normal BAM file index.
- ``CNVSomaticPairWorkflow.normal_bam`` -- (optional, but recommended) Path to normal BAM file. Do not specify in order to run the tumor sample without a matched normal.
- ``CNVSomaticPairWorkflow.normal_bam_idx`` -- (optional, but recommended) Path to normal BAM file index. Do not specify in order to run the tumor sample without a matched normal.
- ``CNVSomaticPairWorkflow.read_count_pon`` -- Path to read-count PoN created by the panel workflow.
- ``CNVSomaticPairWorkflow.ref_fasta_dict`` -- Path to reference dict file.
- ``CNVSomaticPairWorkflow.ref_fasta_fai`` -- Path to reference fasta fai file.
- ``CNVSomaticPairWorkflow.ref_fasta`` -- Path to reference fasta file.
- ``CNVSomaticPairWorkflow.tumor_bam`` -- Path to tumor BAM file.
- ``CNVSomaticPairWorkflow.tumor_bam_idx`` -- Path to tumor BAM file index.

In additional, there are several task-level parameters that may be set by advanced users as above.
Additionally, there are several task-level parameters that may be set by advanced users as above.

To invoke Oncotator on the called tumor copy-ratio segments:

Expand Down