Dear all, I would appreciate having a piece of advice :
how shall I filter a VCF file in order to exclude the GERMLINE and TUMOR samples that have a GENOTYPE of "./".
in R/BioC, for example, if we aim to see the GENOTYPES in the vcf file, we receive the following messages :
> geno(vcf)$GT[,"TUMOR"]
Error in geno(vcf)$GT[, "TUMOR"] : subscript out of bounds
> geno(vcf)$GT[,"NORMAL"]
Error in geno(vcf)$GT[, "NORMAL"] : subscript out of bounds
thank you very much !
What tools are you using? "R/BioC" have multiple tools. Can you please give us the exact commands/scripts you're using?
Dear gentlemen, thank you for your replies and help. Here I am posting the R code that I am using to do the filtering of a VCF file that is generated by DELLY and contains INVERSIONs only .. Any suggestions on how to post/link the input VCF file would be welcome. Thank you very much !
Can you give some background on how the VCF was generated?
Please post the program you are using and the sample vcf file.
I will add to the comments from the 3 other great people. R would not be my 'go to' environment for filtering a VCF. To do what you want, just use
bcftools view
with the following parameter: