Question

HaplotypeCaller - only SNPs

0

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7 months ago

lorena9132 ▴ 10

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

HaplotypeCaller GATK • 452 views

ADD COMMENT • link updated 7 months ago by analyst ▴ 50 • written 7 months ago by lorena9132 ▴ 10

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

ADD REPLY • link 7 months ago by analyst ▴ 50

score 1 · Answer 1 · 2024-04-23

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7 months ago

Pierre Lindenbaum 164k

Filter the vcf dowstream after haplotypecaller using bcftools or gatk variantfiltration

ADD COMMENT • link 7 months ago by Pierre Lindenbaum 164k