HaplotypeCaller - only SNPs
Does anyone know how set HaplotypeCaller to only consider SNPs and not indels?
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link
updated
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Bushra Bibi
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written
by
lorena9132 •
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written
by
lorena9132 •
1 answer
Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration
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Pierre Lindenbaum
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After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file (link to command)