bio-variant-calling-filtering-best-practices

name	bio-variant-calling-filtering-best-practices
description	Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.
tool_type	mixed
primary_tool	bcftools

Variant Filtering Best Practices

Filter Selection Decision Tree

Is dataset large enough for VQSR? (>30 exomes or WGS)
├── Yes → Use VQSR (machine learning)
└── No → Use hard filters
    ├── Germline → GATK recommended thresholds
    └── Somatic → Caller-specific filters + manual review

GATK Hard Filter Thresholds

# SNPs
gatk VariantFiltration \
    -R reference.fa \
    -V raw_snps.vcf \
    -O filtered_snps.vcf \
    --filter-expression "QD < 2.0" --filter-name "QD2" \
    --filter-expression "FS > 60.0" --filter-name "FS60" \
    --filter-expression "MQ < 40.0" --filter-name "MQ40" \
    --filter-expression "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" \
    --filter-expression "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum-8" \
    --filter-expression "SOR > 3.0" --filter-name "SOR3"

# Indels
gatk VariantFiltration \
    -R reference.fa \
    -V raw_indels.vcf \
    -O filtered_indels.vcf \
    --filter-expression "QD < 2.0" --filter-name "QD2" \
    --filter-expression "FS > 200.0" --filter-name "FS200" \
    --filter-expression "ReadPosRankSum < -20.0" --filter-name "ReadPosRankSum-20" \
    --filter-expression "SOR > 10.0" --filter-name "SOR10"

Understanding Quality Metrics

Metric	Meaning	Good Value
QD	Quality by Depth	>2 (variant quality normalized by depth)
FS	Fisher Strand	<60 SNP, <200 indel (strand bias)
MQ	Mapping Quality	>40 (RMS mapping quality)
MQRankSum	MQ Rank Sum	>-12.5 (ref vs alt mapping quality)
ReadPosRankSum	Read Position	>-8 (position in read bias)
SOR	Strand Odds Ratio	<3 SNP, <10 indel (strand bias)
DP	Depth	Sample-specific, avoid extremes
GQ	Genotype Quality	>20 (confidence in genotype)

bcftools filter

Soft vs Hard Filtering

# Hard filter (remove variants)
bcftools filter -e 'QUAL<30' input.vcf.gz -o filtered.vcf

# Soft filter (mark, don't remove)
bcftools filter -s 'LowQual' -e 'QUAL<30' input.vcf.gz -o marked.vcf
# Variants failing filter get "LowQual" in FILTER column

# Include instead of exclude
bcftools filter -i 'QUAL>=30' input.vcf.gz -o filtered.vcf

Expression Syntax

Operator	Meaning
<, <=, >, >=	Comparison
=, ==	Equals
!=	Not equals
&&, ||	AND, OR
!	NOT

Aggregate Functions

Function	Description
MIN(x)	Minimum across samples
MAX(x)	Maximum across samples
AVG(x)	Average across samples
SUM(x)	Sum across samples

Common bcftools Filters

# Basic quality filter
bcftools filter -i 'QUAL>30 && DP>10' input.vcf -o filtered.vcf

# Complex filter with multiple metrics
bcftools filter -i 'QUAL>30 && INFO/DP>10 && INFO/DP<500 && \
    (INFO/FS<60 || INFO/FS=".") && INFO/MQ>40' input.vcf -o filtered.vcf

# Genotype-level filters
bcftools filter -i 'FMT/DP>10 && FMT/GQ>20' input.vcf -o filtered.vcf

# Remove filtered sites
bcftools view -f PASS input.vcf -o passed.vcf

# Keep only biallelic SNPs
bcftools view -m2 -M2 -v snps input.vcf -o biallelic_snps.vcf

# Check for missing values
bcftools filter -e 'QUAL="."' input.vcf.gz  # Exclude missing QUAL
bcftools filter -i 'INFO/DP!="."' input.vcf.gz  # Include only if DP exists

bcftools view Filtering

Filter by Variant Type

# SNPs only
bcftools view -v snps input.vcf.gz -o snps.vcf.gz

# Indels only
bcftools view -v indels input.vcf.gz -o indels.vcf.gz

# Exclude SNPs
bcftools view -V snps input.vcf.gz -o no_snps.vcf.gz

Filter by Region

bcftools view -r chr1:1000000-2000000 input.vcf.gz -o region.vcf.gz

# Multiple regions
bcftools view -r chr1:1000-2000,chr2:3000-4000 input.vcf.gz

Filter by Samples

# Include samples
bcftools view -s sample1,sample2 input.vcf.gz -o subset.vcf.gz

# Exclude samples
bcftools view -s ^sample3,sample4 input.vcf.gz -o subset.vcf.gz

Depth Filtering

# Calculate depth percentiles
bcftools query -f '%DP\n' input.vcf | \
    sort -n | \
    awk '{a[NR]=$1} END {print "5th:", a[int(NR*0.05)], "95th:", a[int(NR*0.95)]}'

# Filter to middle 90% of depth distribution
bcftools filter -i 'INFO/DP>10 && INFO/DP<200' input.vcf -o depth_filtered.vcf

Allele Frequency Filters

# Minor allele frequency filter (population data)
bcftools filter -i 'INFO/AF>0.01 && INFO/AF<0.99' input.vcf -o maf_filtered.vcf

# Allele balance for heterozygotes
bcftools filter -i 'GT="het" -> (AD[1]/(AD[0]+AD[1]) > 0.2 && AD[1]/(AD[0]+AD[1]) < 0.8)' \
    input.vcf -o ab_filtered.vcf

Region-Based Filtering

# Exclude problematic regions
bcftools view -T ^blacklist.bed input.vcf -o filtered.vcf

# Keep only exonic regions
bcftools view -R exons.bed input.vcf -o exonic.vcf

Sample-Level Filtering

# Missing genotype rate per sample
bcftools stats -s - input.vcf | grep ^PSC | cut -f3,14

# Filter samples with >10% missing
bcftools view -S good_samples.txt input.vcf -o sample_filtered.vcf

# Filter sites with >5% missing genotypes
bcftools filter -i 'F_MISSING<0.05' input.vcf -o site_filtered.vcf

Variant Type-Specific Filters

# Separate SNPs and indels for different filters
bcftools view -v snps input.vcf -o snps.vcf
bcftools view -v indels input.vcf -o indels.vcf

# Apply different thresholds
bcftools filter -i 'QUAL>30 && INFO/FS<60' snps.vcf -o snps_filtered.vcf
bcftools filter -i 'QUAL>30 && INFO/FS<200' indels.vcf -o indels_filtered.vcf

# Merge back
bcftools concat snps_filtered.vcf indels_filtered.vcf | bcftools sort -o merged.vcf

Multi-Step Pipeline Filtering

bcftools filter -e 'QUAL<30' input.vcf.gz | \
    bcftools filter -e 'INFO/DP<10' | \
    bcftools view -v snps -Oz -o filtered_snps.vcf.gz

# Named soft filters
bcftools filter -s 'LowQual' -e 'QUAL<30' input.vcf.gz | \
    bcftools filter -s 'LowDepth' -e 'INFO/DP<10' -Oz -o marked.vcf.gz

# Later, remove all filtered variants
bcftools view -f PASS marked.vcf.gz -Oz -o pass_only.vcf.gz

Somatic Variant Filters

# Mutect2 specific
gatk FilterMutectCalls \
    -R reference.fa \
    -V mutect2_raw.vcf \
    --contamination-table contamination.table \
    --tumor-segmentation segments.table \
    -O mutect2_filtered.vcf

# Additional somatic filters
bcftools filter -i 'INFO/TLOD>6.3 && FMT/AF[0]>0.05 && FMT/DP[0]>20' \
    mutect2_filtered.vcf -o somatic_final.vcf

Python Filtering (cyvcf2)

from cyvcf2 import VCF, Writer
import numpy as np

vcf = VCF('input.vcf.gz')
writer = Writer('filtered.vcf', vcf)

for variant in vcf:
    qual = variant.QUAL or 0
    dp = variant.INFO.get('DP', 0)
    fs = variant.INFO.get('FS', 0)
    mq = variant.INFO.get('MQ', 0)

    if qual >= 30 and dp >= 10 and fs <= 60 and mq >= 40:
        writer.write_record(variant)

writer.close()
vcf.close()

Filter by Genotype

from cyvcf2 import VCF, Writer

vcf = VCF('input.vcf.gz')
writer = Writer('filtered.vcf', vcf)

for variant in vcf:
    # Keep if at least one sample is heterozygous
    # gt_types: 0=HOM_REF, 1=HET, 2=UNKNOWN, 3=HOM_ALT
    if 1 in variant.gt_types:
        writer.write_record(variant)

writer.close()
vcf.close()

Filter by Sample Depth

from cyvcf2 import VCF, Writer
import numpy as np

vcf = VCF('input.vcf.gz')
writer = Writer('filtered.vcf', vcf)

for variant in vcf:
    depths = variant.format('DP')
    if depths is not None and np.min(depths) >= 10:
        writer.write_record(variant)

writer.close()
vcf.close()

Validate Filtering

# Compare before/after stats
bcftools stats input.vcf > before_stats.txt
bcftools stats filtered.vcf > after_stats.txt

# Ti/Tv ratio (should be ~2.1 for WGS, ~2.8-3.3 for exomes)
bcftools stats filtered.vcf | grep 'TSTV'

# Count variants per filter
bcftools query -f '%FILTER\n' filtered.vcf | sort | uniq -c

Quick Reference

Task	Command
Quality filter	bcftools filter -e 'QUAL<30' in.vcf.gz
Depth filter	bcftools filter -e 'INFO/DP<10' in.vcf.gz
SNPs only	bcftools view -v snps in.vcf.gz
Indels only	bcftools view -v indels in.vcf.gz
PASS only	bcftools view -f PASS in.vcf.gz
Soft filter	bcftools filter -s 'LowQ' -e 'QUAL<30' in.vcf.gz
Region	bcftools view -r chr1:1-1000 in.vcf.gz
Biallelic	bcftools view -m2 -M2 in.vcf.gz

Common Errors

Error	Cause	Solution
no such INFO tag	Tag not in VCF	Check header with bcftools view -h
syntax error	Invalid expression	Check operator syntax (|| not or)
empty output	Filter too strict	Relax thresholds

Related Skills

• variant-calling/variant-calling - Generate VCF files
• variant-calling/gatk-variant-calling - GATK VQSR
• variant-calling/variant-annotation - Annotation after filtering
• variant-calling/vcf-statistics - Evaluate filter effects