pull out flanking sequences of snp

Question: pull out flanking sequences of snp

4.8 years ago by

myprogramming2016 • 0

myprogramming2016 • 0 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

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modified 4.8 years ago by jwala • 0 • written 4.8 years ago by myprogramming2016 • 0

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 REPLY • link written 4.8 years ago by WouterDeCoster ♦ 45k

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 REPLY • link modified 4.8 years ago • written 4.8 years ago by myprogramming2016 • 0

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

Thanks

ADD REPLY • link written 4.8 years ago by myprogramming2016 • 0

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 REPLY • link written 4.8 years ago by Matt Shirley ♦ 9.5k

4.8 years ago by

myprogramming2016 • 0

myprogramming2016 • 0 wrote:

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

Thanks

ADD COMMENT • link written 4.8 years ago by myprogramming2016 • 0

4.8 years ago by

alexisdereeper • 30

alexisdereeper • 30 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 COMMENT • link written 4.8 years ago by alexisdereeper • 30

4.8 years ago by

Matt Shirley ♦ 9.5k

Cambridge, MA

Matt Shirley ♦ 9.5k wrote:

You could use the FastaVariant class in pyfaidx:

ADD COMMENT • link written 4.8 years ago by Matt Shirley ♦ 9.5k

4.8 years ago by

jwala • 0

jwala • 0 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 COMMENT • link written 4.8 years ago by jwala • 0

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