Questions tagged [snpeff]

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Understanding snpSift/snpEff output

I am trying to check the concordance between two VCF files. Each file contains the same samples, with one being a sequencing experiment, and the other having been genotyped by SNP array. I used snpEff/...
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Questions regarding the detection of variants (SNPs and Indels) in mammal

Greetings, I’m a newbie in bioinformatics working currently on my first project regarding detection of variants (SNPs and Indels) in mammal assembly genome. I used the following method to detect ...
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How to use -csvStats option?

I'm trying to get CSV files from snpEff -csvStats option and got stuck. I tried the code below and only got the vcf file with no contents. How can I use -csvStats option properly? ...