Extract sequences flanking SNPs from organism without reference genome

Question

[konanamenanjacky]

Hi, I'm new in managing DNA sequences and I'm looking for help. I have fastq and vcf files from the sequencing of my samples. The plant species on which I work (Lagenaria siceraria) has no reference genome. What I want to do is to extract SNPs flanking sequences and make a blast in Plant RefSeq for determining the putative functions of my SNPs. All the posts Ive read are related to species that have model organism. Then, could someone help me please?

Thanks

[Denise CS]

Would you also have the GTF file? If so you could try the Variant Effect Predictor. You can annotate the variants if you have the fasta and the gtf. Check the help on cache and database.

[konanamenanjacky]

Thanks, No I don't have the GTF file.

[harold.smith.tarheel]

How was your VCF generated without a reference? Contig assembly then alignment? Alignment to related species reference?

[konanamenanjacky]

Thank Harold, It is GBS, so DNA was digested with ApeKI and final libraries were sequenced using illumina. Alignement was done on partialy sequenced genome (made of contigs, so not annotated) of my species.

Thank a lot for your help

Answer 1

[harold.smith.tarheel]

You can use BEDtools 'slop' to create a BED file of the flanking coordinates, then 'getfasta' to extract the sequences.

Note: this will require the refence contigs to which the reads were aligned.

[konanamenanjacky]

Thanks a lot Harold, I will try and keep you informed!

[konanamenanjacky]

Thanks a lot Harold, It's works very well!