VAT Performance / Reliability Improvements #7828
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gbggrant
approved these changes
May 4, 2022
| ## remove those rows (that match up to the first 5 cols) | ||
| zgrep -v -wFf duplicates.tsv ~{normalized_vcf} > deduplicated.vcf.gz | ||
| rm ~{normalized_vcf} ## clean up | ||
| bcftools query normalized.filtered.bcf -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\n' | sort check_duplicates.tsv | uniq -d | cut -f1,2,3,4,5 > duplicates.tsv |
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I think this can be simplified to:
grep -v '^#' normalized.filtered.bcf | cut -f 1-5 | sort | uniq -d > duplicates.tsv
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and actually we dont need ID either so we could do it with f1,2,4,5
Codecov Report
@@ Coverage Diff @@
## ah_var_store #7828 +/- ##
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Coverage ? 86.305%
Complexity ? 35195
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Files ? 2170
Lines ? 164837
Branches ? 17774
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Hits ? 142262
Misses ? 16253
Partials ? 6322 |
rsasch
approved these changes
May 5, 2022
RoriCremer
approved these changes
May 5, 2022
This was referenced Mar 17, 2023
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