Aligning transcript with known position for SNP to draft genome to find the position of SNPs

Question

[dasakan]

Hi, I have assembled transcriptome (sequenced by RNAseq) with known position of SNPs (Vcf file is there). In the mean time, I have received the draft genome in different scaffolods. To design probe to amplify the SNP target, I am interested to use the genome sequences, however, I donot know the SNP locus in genome. Is there any tool, to align the transcripts in the draft genome and extract the corresponding SNP position within the scaffold sequences keeping the info of respective transcript ids too? It may be like BED coordinates of transcripts in the draft genome.

Answer 1

[Vitis]

Both BLAST and BLAT may be able to do it. I'd try BLAT first. Then it would be straightforward to parse the BLAT result to match the variant positions.

https://metacpan.org/pod/Bio::Tools::Blat

[dasakan]

Thanks:) will try that way..