Locating SNPs from genes of interest in VCF
1
0
Entering edit mode
8 weeks ago
salman_96 ▴ 60

Hi,

I have generated a vcf file from a pancreatic tumor sample (paired end reads were aligned to the genome). I used this command to generate the vcf file.

bcftools mpileup -O v -f $REF $BAM | bcftools call --ploidy 1 -vm -O v >  variants1.vcf

I am interested in finding snps only from this vcf file. Study background is that there are already some genes of interest present (approx. 250) that are known to be important in pancreatic cancer. The gene list that I have has only gene IDs, symbols and genomic coordinates.

My first request is, how do I filter only SNPs that have good quality from my vcf file?

How can I find SNPs from these genes of interest from databases that I can compare to my results?

And how do I compare them to the vcf file that I have? Will coordinates information help?

Thank you!

vcf coordinates mpileup bcftools snps • 220 views
ADD COMMENT
2
Entering edit mode
8 weeks ago

The same tool that you already use has wide range of utilities to help you filter, query and annotate your file:

The important thing to note is that all along generating the variants is the "easy" part, making sense of them is always more challenging.

ADD COMMENT

Login before adding your answer.

Traffic: 929 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6