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changed pre.py params to work with single gvcf #113

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Mar 1, 2021
Merged

changed pre.py params to work with single gvcf #113

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5 changes: 2 additions & 3 deletions doc/normalisation.md
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ usage: VCF preprocessor [-h] [--location LOCATIONS] [--pass-only]
[--fixchr] [--no-fixchr] [--bcf] [-v] [-r REF]
[-w WINDOW] [--threads THREADS] [--force-interactive]
[--logfile LOGFILE] [--verbose | --quiet] [--filter-nonref]
[--convert-gvcf-truth] [--convert-gvcf-query]
[--convert-gvcf-to-vcf]
input output
```

Expand Down Expand Up @@ -148,8 +148,7 @@ be used on genome VCFs since attempting to convert a standard VCF will
cause all biallelic variants to be filtered out (most of them).

```
--convert-gvcf-truth Convert the truth genome VCF to a standard VCF.
--convert-gvcf-query Convert the query genome VCF to a standard VCF.
--convert-gvcf-to-vcf Convert the input genome VCF to a standard VCF.
```

Runtime behaviour can also be controlled as follows:
Expand Down
9 changes: 3 additions & 6 deletions src/python/pre.py
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Expand Up @@ -242,7 +242,7 @@ def preprocessWrapper(args):
args.threads,
args.gender,
args.somatic_allele_conversion,
convert_gvcf_to_vcf=args.convert_gvcf)
convert_gvcf_to_vcf=args.convert_gvcf_to_vcf)

elapsed = time.time() - starttime
logging.info("preprocess for %s -- time taken %.2f" % (args.input, elapsed))
Expand Down Expand Up @@ -316,12 +316,9 @@ def updateArgs(parser):
parser.add_argument('--filter-nonref', dest='filter_nonref', action="store_true", default=False,
help='Remove any variants genotyped as <NON_REF>.')

parser.add_argument('--convert-gvcf-truth', dest='convert_gvcf_truth', action="store_true", default=False,
help='Convert the truth set from genome VCF format to a VCF before processing.')
parser.add_argument('--convert-gvcf-to-vcf', dest='convert_gvcf_to_vcf', action="store_true", default=False,
help='Convert the input set from genome VCF format to a VCF before processing.')

parser.add_argument('--convert-gvcf-query', dest='convert_gvcf_query', action="store_true", default=False,
help='Convert the query set from genome VCF format to a VCF before processing.')

# genotype handling on chrX.
parser.add_argument("--gender", dest="gender", choices=["male", "female", "auto", "none"], default="auto",
help="Specify sex. This determines how haploid calls on chrX get treated: for male samples,"
Expand Down