BLAST and GFF script to find locations of SNPs

Question

[Kiki_01]

Hi! I found SNPs in transcript using GATK and I need to find their locations in genes. I did the BLAST trascripts to the genome. Does anyone know how should python script looks like if I'm trying to connect together my BLAST results with GFF file to find in which genes SNPs are located? I'd appreciate any help!

Answer 1

[colindaven]

The only way to go is to start again - realign your reads to the genome and call the SNVs using GATK there.

Transcriptome != genome (and this is really important when mapping short reads).

BLAST, GFFs etc is all a wild goosechase with no hope of success in my opinion.

[Kiki_01]

Dear colindaven, thank you for your respond, but that's what i have to do according to my thesis. I have found SNPs in transcript and i need to find their locations in genome using script with BLAST results and GFF file together.