Question: Freebayes variant calling understanding
0
gravatar for User000
5 months ago by
User000380
User000380 wrote:

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

snp freebayes • 185 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by User000380
1

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.

ADD REPLYlink written 5 months ago by Denis190

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

ADD REPLYlink written 5 months ago by User000380

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

ADD REPLYlink written 5 months ago by User000380

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

ADD REPLYlink modified 5 months ago • written 5 months ago by Denis190
1

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.

ADD REPLYlink modified 5 months ago • written 5 months ago by Kevin Blighe63k

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.

ADD REPLYlink written 5 months ago by User000380

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?

ADD REPLYlink written 5 months ago by Kevin Blighe63k
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