Question: Finding pre defined SNPs with bedtools
1
gravatar for Schmendrick
3.0 years ago by
Schmendrick10
Schmendrick10 wrote:

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.

snp bcftools samtools bedtools • 1.1k views
ADD COMMENTlink modified 3.0 years ago by natasha.sernova3.5k • written 3.0 years ago by Schmendrick10

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?

ADD REPLYlink written 2.6 years ago by yarmda0

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?

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k
1
gravatar for natasha.sernova
3.0 years ago by
natasha.sernova3.5k
natasha.sernova3.5k wrote:

See this manual:

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

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

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.5k

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?

ADD REPLYlink written 2.6 years ago by yarmda0

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

ADD REPLYlink written 2.6 years ago by WouterDeCoster39k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1282 users visited in the last hour