Deleted:Difficulty returning appropriate info. with esearch and/or efetch
0
0
Entering edit mode
7 weeks ago
Vincent Laufer ★ 2.4k

Hello,

A few days ago I asked some questions regarding how to find associated genomic data easily.

GenoMax recommended efetch and esearch, as can be seen here: Extract nucleotide sequence from a RefSeq Transcript ID

Since this time I have been using these tools; for some reason, though, I am hitting a snag when pulling genetic variants within a given gene ... I have a couple working versions; for instance, e

esearch -db snp -query "FGFR2" | efetch -format docsum


gives me approximately the right information, but no rsIDs are provided. Other queries also get me close, but for instance without variant annotation information (i.e. this results in a missense).

is there a simple way to emend the above query so it gives me rsID, chr, pos, functional info, and (ideally) more?

TYVM

esearch dbsnp efetch • 113 views