Freebayes variant calling understanding
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2.4 years ago
User000 ▴ 580

Hello,

I am using freebayes to do variant calling in my polyploid species (with ploidy 2 anyway). Before filtering I was looking at the bam file alignment and a vcf file. Could you, please explain what does alleles 2/2, 0/2, 1/2 means? 0/0 is reference allele, 1/1 alternative and 0/1 heterozygote? Because if I filter for biallelic alleles, 2/2, 0/2, 1/2 will be removed, although in bam file I can see a very nice high quality SNP which in vcf results as 2/2.

Moreover, in the situation like this, even if there is only one reference allele with a high mapping quality freebayes would result in a 0/1 call. Any suggestions/explanations? image here

freebayes SNP • 1.3k views
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In some loci you have more than just two alleles and for those loci the caller use notations like 2,3, etc. This variants are multiallelic and were filtered out when you tried to leave only biallelic ones.

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that sounds reasonable, but when I have a look at the loci in bam file, I can see only reference allele and alternative allele, something like this: image here

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Ah I see, so you mean the allele is different from other genotypes!

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Try to check this position in different samples, perhaps you'll find several alternative alleles for that position.

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Please paste the actual entries from the VCF file. I believe that Denis is correct in that these are likely multi-allelic sites. You can split these via the following command:

bcftools norm -m-any

Please report back so that we can close off this thread.

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thank you Kevin, I still haven't found a solution for the second part of my question, but if you want to close the thread, go ahead.

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Oh no, I meant 'close off' in the non-literal sense, i.e., find a solution to the problem. Can you possibly paste here these records from your VCF?

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