Question: pull out flanking sequences of snp
0
gravatar for myprogramming2016
4.8 years ago by
myprogramming20160 wrote:

Hi,

I work on plant species. I would like to get flanking sequences of SNPs from the reference genome and the different bam files.

Any help would be appreciated.

Thanks

snp sequence R • 2.2k views
ADD COMMENTlink modified 4.8 years ago by jwala0 • written 4.8 years ago by myprogramming20160

So you have bam files and a reference genome, and a list of snps (their positions), right? Or do you still need to generate the SNP calls based on the bam files? Do you want the flanking sequences as in the reference genome or as sequenced for your bam files?

ADD REPLYlink written 4.8 years ago by WouterDeCoster45k

Thanks for your reply. I do have SNPs and their positions. I would like to get the flanking sequences in reference as well as in bams.

Thanks

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by myprogramming20160

How can I get snp flanking sequence from the genome file?

Thanks

ADD REPLYlink written 4.8 years ago by myprogramming20160

I'm not sure it makes sense to get the flanking sequence from the BAM files. This would be either the flanking sequence from all the reads at all the variant positions, or a consensus variant call which you presumably have in your VCF/FASTA combination.

ADD REPLYlink written 4.8 years ago by Matt Shirley9.5k
0
gravatar for myprogramming2016
4.8 years ago by
myprogramming20160 wrote:

How can I get snp flanking sequence from the genome file?

Thanks

ADD COMMENTlink written 4.8 years ago by myprogramming20160
0
gravatar for alexisdereeper
4.8 years ago by
alexisdereeper30 wrote:

Do you have a VCF file listing all the SNPs in the reference? If so, you can use the SNiPlay application: http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi Load your VCF file and select the plant genome used as reference. And then export flanking sequences of SNPs...

ADD COMMENTlink written 4.8 years ago by alexisdereeper30
0
gravatar for Matt Shirley
4.8 years ago by
Matt Shirley9.5k
Cambridge, MA
Matt Shirley9.5k wrote:

You could use the FastaVariant class in pyfaidx:

ADD COMMENTlink written 4.8 years ago by Matt Shirley9.5k
0
gravatar for jwala
4.8 years ago by
jwala0
jwala0 wrote:

To get read pairs surrounding a SNP site from a BAM, you might try VariantBam. You can input any number of sites, and add a padding to the SNP if you like: https://github.com/jwalabroad/VariantBam

ADD COMMENTlink written 4.8 years ago by jwala0
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