Filter Germline Mutations From .Vcf

Question

[yliuboston]

Hi everyone, I think I have a .vcf file that have compared one tumor and its matched normal, so I guess the "subtraction" job has been done. But I am not quite sure among all those variants called, which germline mutations that I should be confirmed to use in the following analysis, like filter=pass, or based on DP bigger than a threshold? If I donot have access to a more raw form of data like .bam, is there a standard way to do this based on .vcf? Thanks in advance.

[Alex Paciorkowski]

You might want to ask those who gave you the vcf. It'd be a shame to go down one path of analysis when you don't know exactly what the provenance of your data are, right?

Answer 1

[Sean Davis]

Alex's comment is right on. You'll need to determine exactly what was done. Also, you'll want to get access to the BAM files anyway since you'll probably want (need) the option to visually inspect somatic variants.

[yliuboston]

Thanks for your comment. I got .vcf file from TCGA and they indicated the parameters they used in the header of the vcf file. But those variants are too many for me to further analyze. So I am wondering if there are any protocols to work on exist vcf file because currently I do not have access to bam file.

[Sean Davis]

Well, you'll need to determine what is in the VCF file, what is useful to you, and what you need to add in order to answer your question. For instance, you may need to further annotate the VCF files with coding changes, dbSNP and ESP, SIFT, polyphen, mutationtaster. You may need to filter based on allelic depth per sample, etc. There is no "protocol", unfortunately.

[yliuboston]

Thanks! That really helps a lot!