Entering edit mode
4 months ago
lorena9132
▴
10
Does anyone know how set HaplotypeCaller to only consider SNPs and not indels?
Does anyone know how set HaplotypeCaller to only consider SNPs and not indels?
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file (link to command)