Finding pre defined SNPs with bedtools

Question

[Schmendrick]

Bit of a newbie question here...

I have a dataset of Illumina paired end reads mapped to a reference genome with BWA. The next step which I'm struggling with is to call SNPs from this dataset from an existing input list of SNPs. I know how to use bedtools to call new SNPs and to quality filter the calls ect but I'm just not sure how to ask it to pull out a-priori defined snps from a list of genome locations.

Any suggestions would be greatly appreciated.

[yarmda]

I see the answer you got led you to the bedtools documentation. I've reviewed that, but I can't figure out how to actually call out SNPs rather than how to identify which reads overlap them using bedtools. Did you figure that out?

[WouterDeCoster]

What is the reason you don't do variant calling for your entire genome and then filter the variants down to those which you want?

Answer 1

[natasha.sernova]

See this manual:

http://bedtools.readthedocs.io/en/latest/content/overview.html

and find Comparing features in file “A” and file “B”.

[yarmda]

I've read through the documentation, but I don't understand how this works. BED files contain start and stop positions, right? Does this work like an index pointing back to the actual sequences? If not, wouldn't an intersect between a BAM file and a SNPs.bed file only point out the position of the SNP, rather than identifying whether or not there is a SNP in the BAM file's sequence?

[WouterDeCoster]

OP has a bam file and wants to call SNPs...