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Extract sequences flanking SNPs from organism without reference genome

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

snp blast
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updated by harold.smith.tarheel harold.smith.tarheel • written by konanamenanjacky • konanamenanjacky

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

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written by harold.smith.tarheel harold.smith.tarheel

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

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written by konanamenanjacky • konanamenanjacky

1 answer

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.

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written by harold.smith.tarheel harold.smith.tarheel

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