Np add hla to warp #1643
Np add hla to warp #1643
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all_of_us/hla/README.md
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| ## HLAGenotyping | ||
| #### Background | ||
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| This WDL workflow performs HLA genotyping using three separate tools—HLA-HD, Polysolver, and OptiType—and generates a consensus genotype call. It supports both BAM and CRAM input formats and is designed to isolate HLA regions and call genotypes at high accuracy. |
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"is designed to isolate HLA regions and call genotypes at high accuracy" repeats the previous sentence.
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👍 removed this sentence as its redundant
all_of_us/hla/README.md
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| Key characteristics: | ||
| - Uses GATK to extract and prepare HLA-specific reads. | ||
| - Runs HLA-HD, and conditionally runs Polysolver and OptiType if sufficient allele information is detected. |
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replace "if sufficient allele information is detected" with "when HLA-HD fails to emit a three-field allele".
all_of_us/hla/README.md
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| Key characteristics: | ||
| - Uses GATK to extract and prepare HLA-specific reads. | ||
| - Runs HLA-HD, and conditionally runs Polysolver and OptiType if sufficient allele information is detected. | ||
| - Generates harmonized, two-field genotype calls from all tools. |
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It generates three-field genotypes, and most of the time uses only HLA-HD.
all_of_us/hla/README.md
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| - Generates harmonized, two-field genotype calls from all tools. | ||
| - Outputs a consensus genotype combining results from all callers. | ||
| - Designed for hg38 reference genome. | ||
| - Includes support for Terra-specific input quirks (e.g., `EMPTY_STRING_HACK` for optional fields). |
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This is just a hack necessary to circumvent the outdated version of cromwell that Terra is tied to. It doesn't need to be listed as a characteristic of the workflow.
all_of_us/hla/README.md
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| - `File ref_fasta` – Reference FASTA file | ||
| - `File ref_fai` – FASTA index file | ||
| - `File ref_dict` – Reference dictionary file | ||
| - `File hla_intervals` – Interval list specifying HLA regions |
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Perhaps say "specifying HLA region of chromosome 6"
all_of_us/hla/README.md
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| #### Step 4. Optitype (conditional) | ||
| - If HLA-HD emits at least one two-field genotype, runs Optitype. | ||
| - Genotypes A/B/C loci using paired-end FASTQs. |
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I would say A/B/C genes rather than loci
all_of_us/hla/README.md
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| #### Step 5. Consensus (conditional) | ||
| - If both Polysolver and Optitype ran, generates a consensus genotype: | ||
| - For A/B/C genes, overrides HLA-HD with Polysolver results if Polysolver and Optitype agree. |
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To be precise, HLA-HD and Polysolver emit three-field resolution, while Optitype emits two-field. Optitype and Polysolver override HLA-HD if the two-field Optitype genotype is consistent with the Polysolver three field genotype.
all_of_us/hla/README.md
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| #### Step 5. Consensus (conditional) | ||
| - If both Polysolver and Optitype ran, generates a consensus genotype: | ||
| - For A/B/C genes, overrides HLA-HD with Polysolver results if Polysolver and Optitype agree. | ||
| - For other loci, retains HLA-HD results. |
all_of_us/hla/README.md
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| ## MakeTable | ||
| #### Background | ||
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| This WDL workflow consolidates HLA consensus calls from multiple samples into a single summary table. It generates a tabular output where each row represents a sample and each column represents one HLA allele call. |
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Specify that diploid genotypes are represented by giving each gene two consecutive columns, one for each allele. Homozygous genotypes simply repeat the same allele, once in both columns.
| - `Array[File] consensus_calls` – List of consensus result files, one per sample | ||
| - `Array[String] sample_ids` – List of sample IDs (must be the same length and order as `consensus_calls`) | ||
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| #### Step 1. Combine |
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True! I may keep this as is just to keep formatting consistent between AoU ReadMes.
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