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ribioinfo
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@ribioinfo-9434
Last seen 3.7 years ago
Hi I would like to filter my vcf file for MQRankSum and MQ parameters. I have found the function filterVcf() but I can not understand how to use it for this type of filtering. E.g. if I wanted to filter for MQRankSum > -12.5 and MQ > 40 I could use this function?:
filt_vcf=function(vcf, MQRankSum, MQ) {
info = info(vcf)
info_filt = !is.na(info(vcf)$MQRankSum) & info(vcf)$MQ>MQ
return(vcf[info_filt])
}
Thank you.
Riccardo
Can you edit your question to include what you've done, and then post a comment indicating that you've done so? You mention 'manual' but just in case there is both a vignette and standard help page
?filterVcf.