I have a list of SNP location in a file.
Chromosome position chr01 2387766 chr01 7894895 chr01 9090373 chr02 1103 chr02 15118 chr03 160115 chr03 17804 chr04 190961 chr04 19573921 chr04 20867534
Now I want to extract SNP sequence along with flanking sequence of 200 bases. Output example: ACGTTGTCTTCAAGCTAAAGGCTCGTGGAATGAATGCGGC[G/A]GATCTCGGAAAACTTGGAAGATCAACTACTTTGAAAAGT
Reference genome file is present as a refernceGenome.fasta. How do i go about it.