Need help to find FASTA sequence from dbSNP

Question

[syedahumairagillani]

Hello, I am trying to find a fasta sequence to locate SNP using db SNP but I could not find the fasta sequence. The sequence that I want is shown in picture.

Could anyone tell me the steps how to reach this point? I would be grateful because I am trying to get this for so many days.

[Pierre Lindenbaum]

what does it mean ?

Answer 1

[GenoMax]

Using EntrezDirect you can find the location of this SNP:

$ esearch -db snp -query rs1815739 | esummary | xtract -pattern DocumentSummary -element CHRPOS
11:66560624
11:66560624
11:66560624
11:66560624

Now you know that the snp is located on Chr 11 at 66560624. Now you can get the sequence around this position (+ and - NN nucleotides using bedtools getfasta, samtools faidx

Check --> extract sequence around snp ).

[syedahumairagillani]

Thank you for your response. Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you please guide me how to get fasta sequence??

[GenoMax]

Did you not see the last part in my comment above about how to get the sequence?