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Calculate AB (allele balance) using SnpEff/SnpSift

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,

snpeff snpsift allele balance snp
• 4,126 views • link
written by kirannbishwa01 160

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?

• 1 views • link
written by Istvan Albert 10K

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,

• 1 views • link
written by kirannbishwa01 160

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.

• 1 views • link
written by H.Hasani 101

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,

• 2 views • link
written by kirannbishwa01 160

Then it is time to obtain this skill ;)

• 2 views • link
written by H.Hasani 101

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 !!

• 1 views • link
written by kirannbishwa01 160

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