Updating filter syntax and threshold ?
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 32/100
- Issue type
- Documentation
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- bioinformatics, cli, documentation
Research direction
Review the “Filtering variants” page at https://samtools.github.io/bcftools/howtos/variant-calling.html and compare its examples with the bcftools 1.18 commands and thresholds shown here. Check the G1K dataset as proposed, then update the affected examples only if the syntax or thresholds are confirmed outdated; done means the documentation matches the validated filtering guidance.
Written by the indexing model from the issue text.
Description
I could be very wrong. The syntax and threshold values in the example might be outdated in Filtering variants on https://samtools.github.io/bcftools/howtos/variant-calling.html:
bcftools filter -sLowQual -g3 -G10 \
-e'%QUAL<10 || (RPB<0.1 && %QUAL<15) || (AC<2 && %QUAL<15) || %MAX(DV)<=3 || %MAX(DV)/%MAX(DP)<=0.3' \
calls.vcf.gz
I am using the following on bcftools_filterVersion=1.18+htslib-1.18 with a public GRCh38 dataset from PacBio:
bcftools filter -sLowQual -g3 -G10 \
-e 'QUAL<100 || (RPBZ<0.1 && QUAL<150) || (AC<2 && QUAL<150) || VDB<1.0e-04' \
"${input_vcf}" -Oz -o "${output_dir}/filtered.vcf.gz" --write-index
So might be the other examples in "Filtering variants".
P.S. I am going to try the filter on the G1K dataset next to understand if the filter can be generic enough.
- Dominant language
- C
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- Merged PRs (30d)
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