filter multiple VCF files using snpSift
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6.1 years ago
jan ▴ 170

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.. 

snpSift filter vcf • 2.2k views
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Is there a way to filter all files at one time, rather than filtering each file one by one?

why is the 2nd option a problem?

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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.

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6.1 years ago
h.mon 33k

Why not do a loop? It is not "all at one time", but it automates the "one by one".

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Somehow I wasn't thinking about doing a loop. Thank you for the suggestion

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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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