Exome data analysis
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3.8 years ago
pg_canada • 0

Hi everyone, I'm new to this community and new to this type of analysis, so I apologize if this question is simple. I received WES data from 500 individuals. These data has been filtered and is in .txt files. Each file contains data for rare variants per individual (so 500 txt files total). I want to ask for advice to manage all these data, mainly I've been asked to find variants in known genes for each individual. I have been trying to do some reading but am unsure what is the best software to do this?

Thank you for your help.

wes • 665 views
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Hello pg_canada,

the information you are giving are to general to give you concrete advice. How does your "txt" file looks like? (A vcf file would be much better.) What information are already in the file?

fin swimmer

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Hi,

Thanks finswimmer,

Each .txt file has the following information: genotype of the participant, chromosome and chromosome position, reference allele and alternate allele, gene function, snp rs number, ExAC frequency, esp6500 frequency, 1000g frequency, SIFT score, Polyphen and CADD.

I know that vcf would be much better, but unfortunately .txt is what I have available.

Thank you again for your help.

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