AutomationResearch InfrastructureFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

filtering-best-practices

Maintainer FreedomIntelligence · Last updated April 1, 2026

filtering-best-practices.

OpenClawNanoClawAnalysisReproductionfiltering-best-practicesopenclaw medical skillsadditional scientific toolsfiltering

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/filtering-best-practices

Skill Snapshot

2 min

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.
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".

Source Doc

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)