filter multiple VCF files using snpSift
Hi,
I have several hundreds annonated VCF files (annotated using snpEff). I want to filter out all the low quality and low impact variants in all VCF files. Is there a way to filter all files at one time, rather than filtering each file one by one? I'm planning to use snpSift to filter out the low quality variants.
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Why use a loop? The dbsnp is loaded into memory first, and you would end up reloading the dbsnp into memory N times. There has to be a way to load the dbsnp into memory and apply those annotations to N vcf files. Any help with this?
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jamesmatthewhamilton •
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why is the 2nd option a problem?
I wasn't clear in my question. I wanted to ask how to automatically search a gene in all of my files without having to manually do the same thing for all files. I could just do a loop.