vcf-variant-filtering

npx skills add BioTender-max/awesome-bio-agent-skills --skill vcf-variant-filtering --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# VCF Variant Filtering Guide ## Overview Raw VCF files produced by variant callers (GATK HaplotypeCaller, bcftools mpileup, DeepVariant, etc.) contain a mixture of true variants and artifacts from sequencing errors, alignment issues, and low-coverage regions. Computing summary statistics -- Ts/Tv ratio, variant counts, allele frequency distributions -- on unfiltered data yields unreliable results because false-positive calls disproportionately inflate transversion counts and depress the Ts/Tv ratio. This guide covers how to detect whether a VCF is raw, how to apply appropriate quality filters, when filtering is not appropriate, and how to interpret the resulting statistics correctly. ## Key Concepts ### VCF Quality Scores (QUAL Field) The QUAL column in a VCF file represents the Phred-scaled probability that the variant site is polymorphic. A QUAL score of 30 means a 1-in-1000 chance the call is wrong; a QUAL of 20 means 1-in-100. Variant callers assign QUAL scores based on read evidence, base qualities, and mapping qualities. Low-QUAL variants (below 20-30) are enriched for sequencing errors and alignment artifacts. Filtering on QUAL is the simplest and most widely used first-pas

Count occurrences of each FILTER value
bcftools query -f '%FILTER\n' input.vcf | sort | uniq -c | sort -rn | head
Check if any non-'.' FILTER values exist
bcftools query -f '%FILTER\n' input.vcf | grep -v '^\.$' | head
bcftools stats input.vcf | grep ^TSTV
bcftools stats input.vcf | grep ^SN
bcftools view -i 'QUAL>=30' input.vcf | bcftools stats - > filtered_stats.txt
bcftools view -h input.vcf | grep -E '##(FILTER|source|GATKCommandLine|bcftools)'
bcftools query -f '%QUAL\n' input.vcf | awk '{if($1<30) low++; else high++} END {print "QUAL<30:", low+0, "QUAL>=30:", high+0}'
bcftools view -i 'QUAL>=30' input.vcf -Oz -o filtered.vcf.gz