Question: SNP calling from pooled RNA-seq data
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gravatar for thjnant
4.2 years ago by
thjnant90
Germany
thjnant90 wrote:

Hello,

I need to call SNPs from pooled RNA-seq data. In each pool, I have 2 or 3 individuals. I am following the GATK pipeline for this purpose.

What I wonder about, and this could be due to my lack of understanding of the SNP calling process from pooled data, if for a given position, one sees two alleles, how could one say whether this position is a heterozygote in one of the individuals or whether these two different alleles come from two homozygote individuals?

I would appreciate some comments on this. Thanks.

snp rna-seq • 2.6k views
ADD COMMENTlink modified 4.2 years ago by Khader Shameer18k • written 4.2 years ago by thjnant90
0
gravatar for Devon Ryan
4.2 years ago by
Devon Ryan88k
Freiburg, Germany
Devon Ryan88k wrote:

You actually can't call homo/heterozygote in cases like that, though you can determine if a position is a variant (well, part of the time at least). Even if GATK reports calls like that, you should ignore. In fact, this is a general problem with RNAseq where allele-specific expression can mask an underlying heterozygous haplotype.

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by Devon Ryan88k

Thanks for your comment. From individually sequenced RNA-seq data is possible to see whether an individual is homozygote or heterozygote for a given position especially one can always check the bam files against the reference. But as you said, knowing whether a position is homozygote or heterozygote in pooled samples is impossible, the only information is that this position contains variation in a populations.

ADD REPLYlink written 4.2 years ago by thjnant90
1

No, you can't always tell even in singly sequenced samples. You can call heterozygous sites in those, but not homozygous, since you could also be looking at allele-specific expression. That's among the many issues with using RNAseq for variant calling.

ADD REPLYlink written 4.2 years ago by Devon Ryan88k

Oh, yes, you are right. As one allele may not be expressed, so, then the truly heterozygote position will be called as a homozygote. Well, I should handle the limitations. Thanks again.

ADD REPLYlink written 4.2 years ago by thjnant90
0
gravatar for Khader Shameer
4.2 years ago by
Manhattan, NY
Khader Shameer18k wrote:

We recently published a method "eSNV-Detect" to call genotypes from RNA-seq data. 

Publication here and software here

Please give it a try and let us know if you have any questions

ADD COMMENTlink written 4.2 years ago by Khader Shameer18k
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