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Updating SimpleGermlineTagger and somatic CNV experimental post-proce…
…ssing workflow (#5252) Several experimental changes that improve precision results, and expand possible evaluations, of GATK CNV: - `combine_tracks.wdl` for post-processing somatic CNV calls. This wdl will perform two operations: - Increase precision by removing: - germline segments. As a result, the WDL requires the matched normal segments. - Areas of common germline activity or error from other cancer studies. - Convert the tumor model seg file to the same format as AllelicCapSeg, which can be read by ABSOLUTE. This is currently done inline in the WDL. - This is not a trivial conversion, since each segment must be called whether it is balanced or not (MAF =? 0.5). The current algorithm relies on hard filtering and may need updating pending evaluation. - For more information about AllelicCapSeg and ABSOLUTE, see: - Carter et al. *Absolute quantification of somatic DNA alterations in human cancer*, Nat Biotechnol. 2012 May; 30(5): 413–421 - https://software.broadinstitute.org/cancer/cga/absolute - Brastianos, P.K., Carter S.L., et al. *Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets* (2015) Cancer Discovery PMID:26410082 - Changes to GATK tools to support the above: - `SimpleGermlineTagger` now uses reciprocal overlap to in addition to breakpoint matching when determining a possible germline event. This greatly improved results in areas near centromeres. - Added tool `MergeAnnotatedRegionsByAnnotation`. This simple tool will merge genomic regions (specified in a tsv) when given annotations (columns) contain exact values in neighboring segments and the segments are within a specified maximum genomic distance. - `multi_combine_tracks.wdl` and `aggregate_combine_tracks.wdl` which run `combine_tracks.wdl` on multiple pairs and combine the results into one seg file for easy consumption by IGV.
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scripts/unsupported/combine_tracks_postprocessing_cnv/aggregate_combined_tracks.wdl
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| # Unsupported workflow that concatenates the IGV compatible files generated by multiple runs of combine_tracks.wdl | ||
| workflow AggregateCombinedTracksWorkflow { | ||
| String group_id | ||
| Array[File] tumor_with_germline_filtered_segs | ||
| Array[File] normals_igv_compat | ||
| Array[File] tumors_igv_compat | ||
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| call TsvCat as TsvCatTumorGermlinePruned { | ||
| input: | ||
| input_files = tumor_with_germline_filtered_segs, | ||
| id = group_id + "_TumorGermlinePruned" | ||
| } | ||
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| call TsvCat as TsvCatTumor { | ||
| input: | ||
| input_files = tumors_igv_compat, | ||
| id = group_id + "_Tumor" | ||
| } | ||
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| call TsvCat as TsvCatNormal { | ||
| input: | ||
| input_files = normals_igv_compat, | ||
| id = group_id + "_Normal" | ||
| } | ||
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| output { | ||
| File cnv_postprocessing_aggregated_tumors_pre = TsvCatTumor.aggregated_tsv | ||
| File cnv_postprocessing_aggregated_tumors_post = TsvCatTumorGermlinePruned.aggregated_tsv | ||
| File cnv_postprocessing_aggregated_normals = TsvCatNormal.aggregated_tsv | ||
| } | ||
| } | ||
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| task TsvCat { | ||
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| String id | ||
| Array[File] input_files | ||
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| command <<< | ||
| set -e | ||
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| head -1 ${input_files[0]} > ${id}.aggregated.seg | ||
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| for FILE in ${sep=" " input_files} | ||
| do | ||
| egrep -v "CONTIG|Chromosome" $FILE >> ${id}.aggregated.seg | ||
| done | ||
| >>> | ||
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| output { | ||
| File aggregated_tsv="${id}.aggregated.seg" | ||
| } | ||
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| runtime { | ||
| docker: "ubuntu:16.04" | ||
| memory: "2 GB" | ||
| cpu: "1" | ||
| disks: "local-disk 100 HDD" | ||
| } | ||
| } |
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