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Fix Typo
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There was a typo in the annotation of the simple repeats. This lead to problem that the simple repeat annotation was not used in the prioritization step. This error only occurred when the annotation was initiated through AIdiva, otherwise if AIdiva was run on already annotated data there shouldn't be any problem.
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dboceck authored Apr 25, 2022
1 parent 658b363 commit 0927b9a
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion aidiva/variant_annotation/annotate_with_vep.py
Original file line number Diff line number Diff line change
Expand Up @@ -143,7 +143,7 @@ def annotate_from_bed(input_vcf_file, output_vcf_file, annotation_dict, num_core
tmp_repeatmasker.close()

subprocess.run(f"{command} -bed {bed_annotation['segmentDuplication']} -name SegDup -sep '&' -in {input_vcf_file} -out {tmp_segDup.name} -threads {num_cores}", shell=True, check=True)
subprocess.run(f"{command} -bed {bed_annotation['simpleRepeat']} -name SimpleRepeat -sep '&' -in {tmp_segDup.name} -out {tmp_simpleRepeat.name} -threads {num_cores}", shell=True, check=True)
subprocess.run(f"{command} -bed {bed_annotation['simpleRepeat']} -name SimpleRepeats -sep '&' -in {tmp_segDup.name} -out {tmp_simpleRepeat.name} -threads {num_cores}", shell=True, check=True)
subprocess.run(f"{command} -bed {bed_annotation['oe_lof']} -name oe_lof -sep '&' -in {tmp_simpleRepeat.name} -out {tmp_oe_lof.name} -threads {num_cores}", shell=True, check=True)

if os.path.isfile(bed_annotation["omim"]):
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