Update vcf file processing #124
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Fnyasimi
reviewed
Feb 7, 2022
| @@ -8,7 +8,7 @@ | |||
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| def vcf_file_geno_lines(path, mode="genotyped", variant_mapping=None, whitelist=None, skip_palindromic=False, liftover_conversion=None): | |||
| logging.log(9, "Processing vcf %s", path) | |||
| vcf_reader = VCF(path) | |||
| vcf_reader = VCF(path, gts012=True) | |||
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What does gts012 represent?
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From cyvcf2.VCF documentation:
gts012 (bool) – if True, then gt_types will be 0=HOM_REF, 1=HET, 2=HOM_ALT, 3=UNKNOWN. If False, 3, 2 are flipped.
Fnyasimi
reviewed
Feb 7, 2022
| yield (variant_id, chr, pos, ref, alt, f) + tuple(d) | ||
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| elif mode == "imputed": | ||
| if len(alts) > 1: | ||
| logging.log("VCF imputed mode doesn't support multiple ALTs, skipping %s", variant_id) | ||
| if (len(ref)) | (len(alts[0])) > 1: |
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The genotype contains indels too?
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Yes, and they could be coded as either REF or ALT.
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I made some edits to get Predict.py running on UK Biobank data converted to VCF format. Note, I used plink2 to convert bgen to vcf with the modifer 'vcf-dosage=DS-force'. Otherwise, dosages were missing from genotyped variants if I used 'vcf-dosage=DS'.