Should haplotypes or primitive SNPs be used for RAiSD input?

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Brian Mack

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Jun 2, 2020, 12:16:32 PM6/2/20

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Hi, I'm identifying SNPs using Freebayes, which outputs haplotype calls instead of individual SNPs. I noticed that if I run vcfallelicprimitives on the vcf, which breaks apart the MNPs, and provide that to RAiSD I get somewhat different results. Is there a recommended format of the SNPs that should be provided to RAiSD?

Thanks,

Brian

Nikolaos Alachiotis

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Jun 3, 2020, 11:37:20 AM6/3/20

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Hi Brian,

The following three conditions must be satisfied for a VCF line to not be straight away discarded by RAiSD:

a) REF field contains a single character

b) ALT field contains a single character,

c) Either GT or GP/GL are present in the FORMAT field

Nikos

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