Question: Variant calling results in polyploidy data
1
gravatar for mufernando
4.1 years ago by
mufernando10
Brazil
mufernando10 wrote:

Hi,

I ran CRISP to do the variant calling in some Drosophila pooled samples and when I try to filter for minimum allele frequency with vcftools I get the following error:

VCFtools - 0.1.14
(C) Adam Auton and Anthony Marcketta 2009

Parameters as interpreted:
    --vcf new_variantcalls.vcf
    --maf 0.15
    --out berg

After filtering, kept 14 out of 14 Individuals
Error: Polyploidy found, and not supported by vcftools: YHet:49

Does anybody know how to fix this?

I run the grep command Pierre suggested and this is the output is here: https://jpst.it/MUgG

crisp vcftools next-gen pool-seq • 2.0k views
ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by mufernando10

please, validate or comment your previous questions:

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum131k

Thanks for the heads up. I'll do that.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by mufernando10

That is not possible as no one answered my questions.

ADD REPLYlink written 4.1 years ago by mufernando10

I've moved the 'comments' to 'answers' for the two first items.

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum131k
3
gravatar for Pierre Lindenbaum
4.1 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

looking at the vcftools source code: https://github.com/kiwiroy/vcftools/blob/master/cpp/vcf_entry_setters.cpp#L97

        if (pos != pos2)
LOG.error("Polyploidy found, and not supported by vcftools: " + CHROM + ":" + header::int2str(POS));

you have a strange genotype in CHROM= YHet at POS = 49. (something that doesn't look like '([0-9]+/[0-9]+)'. I suppose you have more than two alleles for a Genotype

please, show us the output of

 grep -v "^#"  new_variantcalls.vcf | cut -f 10- | cut -d ':' -f 1 | sort | uniq

Does anybody know how to fix this?

change the way your VCF is called. ...

ADD COMMENTlink written 4.1 years ago by Pierre Lindenbaum131k

I edited the original post

ADD REPLYlink written 4.1 years ago by mufernando10

and as you can see, this is not a diploid genotype. You have

0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0

ploidy=48

while vcftools expects something like a diploid genotype ( e.g: 0/0 ) to calculate the MAF

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by Pierre Lindenbaum131k

Would you say this is a problem with the variant caller or with sth that I performed before (e.g., alignment, local realignment)? If something could have happened before how can I check?

ADD REPLYlink written 4.1 years ago by mufernando10

Would you say this is a problem with the variant caller

sorry, I don't know "CRISP".

ADD REPLYlink written 4.1 years ago by Pierre Lindenbaum131k

Hi I am getting the same error of "Error: Polyploidy found, and not supported by vcftools "6:6292579"

The output of

grep -v "^#" chr6.vcf | cut -f 10- | cut -d ':' -f 1 |sort | uniq

is giving : " 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 0|0 "

which means it is a diploid genotype only. What could be the reason for the error then?

ADD REPLYlink written 3.0 years ago by shrutishreyajha0
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