pull out flanking sequences of snp

Question

[myprogramming2016]

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

[WouterDeCoster]

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?

[myprogramming2016]

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

[myprogramming2016]

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

Thanks

[Matt Shirley]

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.

Answer 1

[myprogramming2016]

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

Thanks

Answer 2

[alexisdereeper]

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...

Answer 3

[Matt Shirley]

You could use the FastaVariant class in pyfaidx:

Answer 4

[jwala]

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