SnpSift match overlapping mutations with a given bed file

Question

[morovatunc]

Hi,

I know how to get overlapping mutations in my vcf with a given bed file. But is there a way to get a simple number from a log file ? like in the vcftools ?

Best,

Tunc.

[Medhat]

can you give example of what exactly you want

[morovatunc]

On one hand I have bed file. On the other hand I have my vcf file.

I want to extract mutations on that vcf file within that bed file locations as a VCF + I want to know how many of them are there.

Thank you for your response.

Tunc.

[Medhat]

Did you tried bedtools intersect -a yourVcfFile.vcf -b yourBed.bed > result.vcf

and for how many "number of lines" wc -l result.vcf

If I understood right your question.

[morovatunc]

With this method I got that number that I want, but I will try to keep it as a last option because snpsift itself can do that isolation as well, I just wanted to know if it has a option like vcftools's log file.

Thank you very much for your useful solution.

[Medhat]

I think yes, you will need to use one of those according to your needs

• countHom() Count number of homozygous genotypes No arguments (countHom() > 0)
• countHet() Count number of heterozygous genotypes No arguments (countHet() > 2)
• countVariant() Count number of genotypes that are variants (i.e. not reference 0/0) No arguments (countVariant() > 5)
• countRef() Count number of genotypes that are NOT variants (i.e. reference 0/0)