SAMTools and BED files

[ashkot]

Hi there,
I am interested in looking at only certain SNP from the human genome and for each of them I have the chromosomal info and coordinate in both HG18 and HG19 systems.

When analyzing the full genome using SAMTools can i somehow specify my variants of interest in BED (or some other format) and the output VCF would only have all of those or subset of my variants.

This way I can keep the VCF file size down which would make it easy to parse it.

Thanks,
A

[swbarnes2]

Hi there,
I am interested in looking at only certain SNP from the human genome and for each of them I have the chromosomal info and coordinate in both HG18 and HG19 systems.

When analyzing the full genome using SAMTools can i somehow specify my variants of interest in BED (or some other format) and the output VCF would only have all of those or subset of my variants.

This way I can keep the VCF file size down which would make it easy to parse it.

Thanks,
A

You can use BEDTools to intersect a .bed file with a .vcf file. You'd have to make an all-points vcf first.

You can also intersect .bed files with .bam files, but I don't think that is what you want. You'll get all the .bam entries that cross your .bed locations, but it won't narrow down to just that single base of the .bed interval.