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Is bcftools merge a right choice to combine three rice populations?

Hello Everyone,

I have performed genotyping for three rice populations separately, using GATK pipeline. and now I want to merge these three gvcf files for further GWAS analysis. Will it be right strategy to use bcftools merge to combine these three populations? Please share your thoughts on this. Appreciate your time.

Thank you in advance.

Sincerely, CK

bcftools rice haplotypecaller populations gatk
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written by Chander Kant Chaudhary 1

1 answer

if you used the " GATK pipeline" then you should have produced GVCF files using HaplotypeCaller in ERC mode. The GVCF must be then loaded using "gatk GenomicDBImport" and joint-genotyped using "gatk GenotypeGVCFs"

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written by Pierre Lindenbaum 17K

Thank you @Pierre Lindenbaum for the response. I have used the GATK pipeline only using the mentioned steps. But I ran GenotypeGVCFs separately on these populations instead on the combine (Pop1+ Pop2 + Pop3) gvcf file. Are you suggesting to perfomr the genotyping using GenotypeGVCFs on combine populaiton file?

Thank you in advance.

• 0 views • link
written by Chander Kant Chaudhary 1

yes, you need to combine all the population into one gvcf using GenomicDBImport+GenotypeGVCFs

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written by Pierre Lindenbaum 17K

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