Entering edit mode
ribioinfo
▴
100
@ribioinfo-9434
Last seen 4.2 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
.