Hi,
I've been trying to obtain SNPs that have a MAF > 5% with the UCSC Table Browser. I tried using a free-form query of:
minorAlleleFreq > 0.05
but the SNP output is the same each time, and does not seem to have been filtered (2nd last row of sample has a MAF < 0.05).
chrom chromStart chromEnd name minorAlleleFreq
Filtering on 0 columns
chr1 10177 10179 rs367896724 0.425319,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,
chr1 10352 10353 rs555500075 0.4375,-inf,-inf,-inf,-inf,0.00381679,-inf,-inf,-inf,-inf,-inf,-inf,
chr1 11007 11008 rs575272151 0.0880591,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,
chr1 11011 11012 rs544419019 0.0880591,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,
chr1 13109 13110 rs540538026 0.0267572,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,
chr1 13115 13116 rs62635286 0.0970447,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,-inf,
Screenshot of Filter section:
•
written
by
dumeir •
1 answer
Hello,
Unfortunately, there is no way to complete this query on the Table Browser. As RamRS pointed out, the minorAlleleFreq field dbSnp153Common.bb is not a numeric column. It is an array indexed by frequency-reporting project, with 1000Genomes first, which should comprise most all of the > 5% variants.
You can, however, use the bigBedToBed utility from the command line, supplying the URL to the UCSC download server directly to get the information you are looking for. Our utilities can be found here: http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads
Once you have downloaded the utility for your respective operating system, you can run the following on your terminal to extract all the variants from the 1000 Genomes project with minor allele frequency > 5%:
bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp153Common.bb stdout | \
awk -F"\t" '
{ tgpFreq = $10;
sub(/,.*/, "", tgpFreq);
if (tgpFreq > 0.05) {print;}
}' > dbSnp153_1000Genomes_Gt5Pct.bed
If you have any follow up questions, our help desk can always be reached at genome@soe.ucsc.edu. You may also send questions to genome-www@soe.ucsc.edu if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.
•
written
by
Luis Nassar
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Thanks for your help!
The table schema shows that
minorAlleleFreqis not a numeric column that can be filtered using the sort of simple free form query that you're using. I'm not sure how to achieve what you want.