Hi,
My field is not bioinformatics and I am facing some problems in exome sequencing data analysis. I want to know about variants prioritization methods. when we are applying filtration parameters in exome sequencing data files to separate heterozygous and homozygous variants and further filter into stop/gain, frameshift, splicing, and missense variants. So initially the MAF (minor allele frequency ) threshold we keep is 0.01 or 0.001 ?? . I am a bit confused about how much MAF I should set initially for filtering rare variants from the exome file. And is there any different criteria for heterozygous and homozygous variant filteration or same parameters will be kept in the filtration process, like Mutation taster score, polyphen2, CADD, sift, FATHMM and M-CAP? .
Kindly suggest to me some good related papers also.
Thanks.
it is best to set MAF threshold at 0.001 but incase you didn't find any variant within this frequency range than you can go for 0.01 frequency range.
i would suggest you to read this article please.
Sefid Dashti, M. J., & Gamieldien, J. (2017). A practical guide to filtering and prioritizing genetic variants. Biotechniques, 62(1), 18-30.
Muhammad Umair
The inheritance pattern is recessive and the disorder is bipolar.
try 0.001, check for number of homozygotes at GnomaAD browser, check for homozygous stretches in exome as pattern of inheritance is recessive
What about dominant and heterozygous mutation? What frequency is acceptable?
Sarmad Mehmood Thanks for the response.
can you briefly explain what do you mean by homozygous stretches?
Aisha Hashmi, you are welcome. Actually in the column where homozygosity is mentioned you can see how long is that column on physical distance, you can find a locus there
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