How to achieve Variant filtering?
Using CLC Genomics Workbench, I have successfully run some fastq sequences and got the 'Final Annotated variants' in an excel sheet. However, I want to filter these to keep and detect only those with actual clinical relevance to Neuroblastoma. Is there a way to do it?
I need to filter out the artifacts using either gnomAD, COSMIC, or REVEL databases, but I do not know how to do it.
Also, is there a way to generate a black list and use the population frequency to filter out the variants?
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Istvan Albert
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Sharanya •
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Sharanya •
1 answer
bcftools offers many utilities to filter variants,
https://samtools.github.io/bcftools/bcftools.html
another alternative is vcflib
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