Question: Calculate AB (allele balance) using SnpEff/SnpSift
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gravatar for kirannbishwa01
4.8 years ago by
kirannbishwa011.3k
United States
kirannbishwa011.3k wrote:

Is it possible to calculate Allele balance for heterozygote genotypes using SnpEff/SnpSift. My thought is yes, but I am not finding any clue.

Thanks,

snp snpeff allele balance snpsift • 1.8k views
ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by kirannbishwa011.3k

snpEff is for detecting the effect of snps not for calling snps. snpSift is a tool for filtering snp information, but for that you need to have those attributes computed and present in the file. Do you have those?

ADD REPLYlink written 4.8 years ago by Istvan Albert ♦♦ 86k

Sorry, I don't have the attributes computed in the vcf file. I used GATK haplotype caller to call the variants (when I could have asked to ouptut the AB parameter but unfortuntely didn't). It takes about 3 days to call the variants on each sample, so wanted to do it post variants calling.

Thanks,

ADD REPLYlink written 4.8 years ago by kirannbishwa011.3k

Hi,

I thought the allele balance is the ratio of reads that support the alternative allele. This information is contained in the vcf file anyway (INFO field) , you just need to calculate it yourself.

ADD REPLYlink written 4.8 years ago by H.Hasani970

Hi Hansani,

Thank you for the info. But GATK haplotypecaller doesn't calculate the AB values unless specified. I have the AD values for ref vs. alt alleles (which can be used to calculate AB values), but I am not finding a way to calculate it. I don't have programming skill, I work on the level of scripts.

Thanks,

ADD REPLYlink written 4.8 years ago by kirannbishwa011.3k

Then it is time to obtain this skill ;)

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by H.Hasani970

HI Hasani,

Thank you for the suggestion. I actually tried to learn some programming skills for python. My background is biology with expertise in evolution. I think it would be quite awesome to be a programmer as well but I have not had enough time to teach myself. And at times I have tried some programming but ended up quite frustrated and unsuccesful. I really want to thank Biostar community for all the help they have been and suggestion they have made while running a program or preparing a script.

I will work on some programming skill but I can't assure that I won't be bothering BioStars community. Lol (; I hope everyone understands !!

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by kirannbishwa011.3k
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