HaplotypeCaller - only SNPs
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27 days ago
lorena9132 ▴ 10

Does anyone know how set HaplotypeCaller to only consider SNPs and not indels?

HaplotypeCaller GATK • 292 views
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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file (link to command)

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27 days ago

Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration

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