BGE gCNV #206
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BGE gCNV #206
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I will test for identical results, and probably add a test as well |
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Results confirmed to be identical to gatk wdl |
rickymagner
approved these changes
Mar 6, 2025
| "CNVCallingAndMergeForFabric.filtered_cnv_genotyped_segments_vcf_md5sum": null, | ||
| "CNVCallingAndMergeForFabric.merged_vcf": { | ||
| "file": "gs://palantir-workflows-test-data/CNVCallingAndMergeForFabric/0437227296_subset.merged.vcf.gz", | ||
| "line_skip_regex": "^##bcftools|^##GATKCommandLine=|^##FORMAT=<ID=GT|^##source=" |
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Why skip the FORMAT=<ID=GT line in the header? Is this not standardized so it fails because there's a different description or something?
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Yes, essentially. It turns out that MergeVcfs in Picard generates a non-deterministic header with respect to which input vcf it will pull the FORMAT=<ID=GT line from. In our case, the header line includes a different description depending on whether it gets pulled from the gcnv vcf or the dragen vcf.
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Pull BGE production pipeline from gatk branch to here.