Question: Filter Germline Mutations From .Vcf
2
gravatar for yliuboston
6.3 years ago by
yliuboston20
yliuboston20 wrote:

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.

vcf • 3.9k views
ADD COMMENTlink modified 6.3 years ago by Sean Davis26k • written 6.3 years ago by yliuboston20
2

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?

ADD REPLYlink written 6.3 years ago by Alex Paciorkowski3.4k
0
gravatar for Sean Davis
6.3 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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.

ADD COMMENTlink written 6.3 years ago by Sean Davis26k

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.

ADD REPLYlink written 6.3 years ago by yliuboston20

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.

ADD REPLYlink written 6.3 years ago by Sean Davis26k

Thanks! That really helps a lot!

ADD REPLYlink written 6.3 years ago by yliuboston20
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