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feat: merge vardict and tnscope (#1475)
#### Changed - Refactored rules for bcftools filters - Renamed final UMI bamfile to ensure hsmetrics are collected in multiqc json - Changed ranked VCF from research to clincial - Lowered min AF for TGA from 0.007 to 0.005 - Lowered maximal SOR for TNscope in TGA tumor only cases from 3 to 2.7 - Changed filter settings for research TNscope vcf, now either PASS or triallelic_site (fixing this issue: #1293) #### Added - TNscope for TGA workflows, merged with VarDict results - New filter for VarDict for tumor in normal contamination - Export TMP environment variables to rules that lack them - Added genmod ranked VCFs to be delivered - Added family-id to genmod in order to get ranked variants to Scout (solved this: #1045) - Added DP and AF to INFO-field of TNscope vcfs for ranking model - Raw TNscope calls and unfiltered research-annotated SNVs to delivery #### Removed - ML-model for TNscope is removed due to license issue with new version of Sentieon - All code associated with TNhaplotyper - Removed research.filtered.pass VCFs from delivery and storage list
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@@ -11,4 +11,4 @@ jobs: | |
| - uses: psf/black@stable | ||
| with: | ||
| options: "--check --verbose" | ||
| version: "22.3.0" | ||
| version: "23.7.0" | ||
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| @@ -0,0 +1,109 @@ | ||
| #!/usr/bin/env python | ||
| import vcfpy | ||
| import click | ||
| import sys | ||
| import logging | ||
| from typing import List, Optional | ||
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| LOG = logging.getLogger(__name__) | ||
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| def summarize_ad_to_dp(ad_list): | ||
| """ | ||
| Summarizes the AD (allelic depth) field into total DP (read depth). | ||
| Parameters: | ||
| ad_list (list): List of read depths supporting each allele, [ref_depth, alt1_depth, alt2_depth, ...] | ||
| Returns: | ||
| int: Total read depth (DP) across all alleles. | ||
| """ | ||
| if ad_list is None: | ||
| return 0 # Return 0 if AD field is not present | ||
| return sum(ad_list) | ||
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| @click.command() | ||
| @click.argument("input_vcf", type=click.Path(exists=True)) | ||
| @click.argument("output_vcf", type=click.Path()) | ||
| def process_vcf(input_vcf: str, output_vcf: str): | ||
| """ | ||
| Processes the input VCF file and writes the updated information to the output VCF file. | ||
| INPUT_VCF: Path to the input VCF file. | ||
| OUTPUT_VCF: Path to the output VCF file. | ||
| """ | ||
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| # Open the input VCF file | ||
| reader: vcfpy.Reader = vcfpy.Reader.from_path(input_vcf) | ||
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| # Ensure the sample name is 'TUMOR' | ||
| sample_name: str = reader.header.samples.names[0] | ||
| if sample_name != "TUMOR": | ||
| LOG.warning( | ||
| f"Error: The first sample is named '{sample_name}', but 'TUMOR' is expected." | ||
| ) | ||
| sys.exit(1) | ||
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| # Add AF and DP fields to the header if not already present | ||
| if "AF" not in reader.header.info_ids(): | ||
| reader.header.add_info_line( | ||
| vcfpy.OrderedDict( | ||
| [ | ||
| ("ID", "AF"), | ||
| ("Number", "A"), | ||
| ("Type", "Float"), | ||
| ("Description", "Allele Frequency"), | ||
| ] | ||
| ) | ||
| ) | ||
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| if "DP" not in reader.header.info_ids(): | ||
| reader.header.add_info_line( | ||
| vcfpy.OrderedDict( | ||
| [ | ||
| ("ID", "DP"), | ||
| ("Number", "1"), | ||
| ("Type", "Integer"), | ||
| ("Description", "Total Depth"), | ||
| ] | ||
| ) | ||
| ) | ||
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| # Open the output VCF file for writing | ||
| with vcfpy.Writer.from_path(output_vcf, reader.header) as writer: | ||
| # Loop through each record (variant) | ||
| for record in reader: | ||
| # Get the TUMOR sample data | ||
| sample_index: int = reader.header.samples.names.index(sample_name) | ||
| tumor_call: vcfpy.Call = record.calls[sample_index] | ||
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| # Check and process AD field | ||
| tumor_ad: Optional[List[int]] = tumor_call.data.get( | ||
| "AD", None | ||
| ) # AD is a list [ref_count, alt_count] | ||
| if tumor_ad is None: | ||
| LOG.warning( | ||
| f"Warning: AD field is missing for record at position {record.POS} on {record.CHROM}" | ||
| ) | ||
| else: | ||
| record.INFO["DP"] = summarize_ad_to_dp(tumor_ad) | ||
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| # Check and process AF field | ||
| tumor_af: Optional[float] = tumor_call.data.get("AF", None) | ||
| if tumor_af is None: | ||
| LOG.warning( | ||
| f"Warning: AF field is missing for record at position {record.POS} on {record.CHROM}" | ||
| ) | ||
| record.INFO["AF"] = [0.0] # Default AF to 0.0 if missing | ||
| else: | ||
| record.INFO["AF"] = [tumor_af] # Wrap AF in a list | ||
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| # Write the updated record to the output VCF file | ||
| writer.write_record(record) | ||
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| click.echo(f"VCF file processed and saved to {output_vcf}") | ||
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| if __name__ == "__main__": | ||
| process_vcf() |
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| @@ -0,0 +1,16 @@ | ||
| #!/usr/bin/awk -f | ||
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| BEGIN { | ||
| ENVIRON["LC_ALL"] = "en_US.UTF-8" | ||
| } | ||
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| # If the line starts with a '#', it's a header, so print it as is | ||
| $1 ~ /^#/ { | ||
| print $0; | ||
| next; | ||
| } | ||
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| # Otherwise, send the body lines to an external sort command | ||
| { | ||
| print $0 | "/usr/bin/sort -k1,1V -k2,2n" | ||
| } |
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