Question: How to add flanking sequences to SNPs from vcf files
gravatar for helge.fluess
3 months ago by
helge.fluess0 wrote:

Hej, I posted this question in Biostars nad would like to shift this post here to biostars galaxy: ello everyone,

I'm new to this community and looking for some help. I applied a variant calling pipeline with RNAseq data of four plant samples. Thus, after mapping each sample to a reference genome using Tophat, i used MPileup for variant calling, including all four samples. While I am content with the results, i wonder if there is any possibility to add the sequence information from the BAM files, to the VCF output of MPileup. I i get it right, the VCF output gives me information about the position of the SNP/Variant on the reference chromosome/contig. Since my goal is to create KASP assays from the SNP information, I'd like to add 100bp in before and after the called SNP. Is this possible, without having to find each position in the contig by hand?

Maybe someone had the same issue before?

Thanks in advance Cheers Helge

rna-seq snp vcf mpileup • 189 views
ADD COMMENTlink modified 3 months ago • written 3 months ago by helge.fluess0
gravatar for Jennifer Hillman Jackson
3 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Convert with NGS: VCF Manipulation > VCFtoTab-delimited. Then assign the more specific interval format and data column attributes.

Adjust the coordinates with Operate on Genomic Intervals > Get flanks returns flanking region/s for every gene (Galaxy Version 1.0.0). It works fine with single base "intervals".

This results in genomic coordinates with respect to the reference genome. If you need fasta data after that use Fetch Alignments/Sequences > Extract Genomic DNA using coordinates from assembled/unassembled genomes.

Galaxy FAQs:

Galaxy Tutorials:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3 months ago by Jennifer Hillman Jackson25k
gravatar for helge.fluess
3 months ago by
helge.fluess0 wrote:

Exactly what i needed. Now i just have to contact our galaxy person in charge (we run a local instance of galaxy) to imnplement the tools needed.

Thanks a ton!

Cheers Helge

ADD COMMENTlink written 3 months ago by helge.fluess0
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