Locating SNPs from genes of interest in VCF

Question

[salman_96]

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!

Answer 1

[Istvan Albert]

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

• http://samtools.github.io/bcftools/bcftools.html

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