Plot with locuszoom and chr:pos SNPs

Question

[alesssia]

Dear all,

I have run a GWAS with PLINK, obtaining, as output, a file with the following format:

CHR SNP A1 A2 TEST AFF UNAFF CHISQ DF P
6 6:131182784 G T ALLELIC 349/429 872/1584 22 1 2.731e-06
6 6:131179801 C G ALLELIC 349/429 874/1582 21.6 1 3.356e-06

and I would like to visualise these results using locuszoom (http://locuszoom.sph.umich.edu/locuszoom/genform.php?type=yourdata). However, I obtain the following warning/error:

WARNING: your association results file has both rsID and chr:pos SNP
names. Please make sure you have selected the correct genome build by
using the --build parameter, or by selecting the appropriate build on
the website.
Error: region specified contains no SNPs, skipping..

Even though I do not have any rsID SNP, the build parameter has been chosen correctly (actually I have tried with every build with no improvement), and there are SNPs in the specified region.

Can anyone help? Thank you very much in advance.

[dhibar]

Can you give a screenshot or more details about the other the options you are selecting in LocusZoom? Is it possible the region and flanking region you specified doesn't include any SNPs from your results list? Or maybe they aren't being read in properly because the default delimiter is "Tab" and your data are spaced?

[alesssia]

Thanks dhibar. The region to be plot has been selected to be the selected region (including 119 SNPs), and the space delimiter has been correctly set to "space" (I used the option "Set for PLINK data"). Column names have been correctly selected as well. Let's say I used the option I have been successfully using for plotting rsID SNPs.

Here are the details:

This is lzplot.php Version 0.8
Input file is '/tmp/phpnj7UJS', 3792 bytes (originally chr13.txt)
Cache file=/tmp/lzplot.4817/m2zfsat.cache.db
CMD=/data/locuszoom/bin/locuszoom/bin/locuszoom --plotonly --verbose --metal /tmp/phpnj7UJS --chr 13 --start 71925000 --end 72066600 --prefix EUR --build hg19 --pop EUR --source 1000G_Nov2014 --delim whitespace --pvalcol P --markercol SNP --snpset NULL --cache /tmp/lzplot.4817/m2zfsat.cache.db geneFontSize=.8 smallDot=.3 largeDot=.9 format=pdf ymax=10 legend=auto metalRug='Plotted SNPs' rfrows=10 weightCol=NULL showRecomb=TRUE warnMissingGenes=T showAnnot=FALSE

WARNING: your association results file has both rsID and chr:pos SNP
names. Please make sure you have selected the correct genome build by
using the --build parameter, or by selecting the appropriate build on
the website.

Error: region specified contains no SNPs, skipping..
Error: no image file found
+---------------------------------------------+
| LocusZoom 1.2 (01/04/2013)                  |
| Plot regional association results           |
| from GWA scans or candidate gene studies    |
+---------------------------------------------+

Loading settings..
Options in effect are:

+----------+-----------------------------------+
|  Option  |               Value               |
+----------+-----------------------------------+
| metal    | phpnj7UJS                         |
| chr      | 13                                |
| start    | 71925000                          |
| end      | 72066600                          |
| build    | hg19                              |
| pop      | EUR                               |
| source   | 1000G_Nov2014                     |
| snpset   | NULL                              |
| cache    | /tmp/lzplot.4817/m2zfsat.cache.db |
| verbose  | True                              |
| plotonly | True                              |
+----------+-----------------------------------+

Plotting parameters in effect are:

+------------------+--------------+
|      Option      |    Value     |
+------------------+--------------+
| ymax             | 10           |
| largeDot         | .9           |
| format           | pdf          |
| markerCol        | SNP          |
| warnMissingGenes | T            |
| geneFontSize     | .8           |
| rfrows           | 10           |
| weightCol        | NULL         |
| showRecomb       | TRUE         |
| pvalCol          | P            |
| showAnnot        | FALSE        |
| legend           | auto         |
| smallDot         | .3           |
| metalRug         | Plotted SNPs |
+------------------+--------------+

Using /lz/bin/locuszoom/bin/locuszoom.R..
Beginning plotting sequence for: chr13_71925000-72066600
Wed Jan 13 09:19:29 2016 Extracting region of interest (chr13:71925000-72066600) from metal file..
Deleting temporary files..
Time required: <1s

Total run time is 1 seconds

[alesssia]

This specific question regarded the online version of LocusZoom (http://locuszoom.org/genform.php?type=yourdata, "Genome Build/LD Population" field). If you use the standalone version, they should be downloaded along with the main app (https://statgen.sph.umich.edu/locuszoom/download/), and you can use it by setting the following parameters --build hg19 --pop EUR --source 1000G_Nov2014. Hope this helps!

[xliu4255]

Hi may I ask how do you get the 1000G_Nov2014 files for LD calculation?

[alesssia]

This specific question regarded the online version of LocusZoom (http://locuszoom.org/genform.php?type=yourdata, "Genome Build/LD Population" field). If you use the standalone version, they should be downloaded along with the main app (https://statgen.sph.umich.edu/locuszoom/download/), and you can use it by setting the following parameters --build hg19 --pop EUR --source 1000G_Nov2014. Hope this helps!

[xliu4255]

Hi Alesssia! Thanks for your help. Because I use standalone version and in that version 1000G_Nov2014 LD reference is not included, so I ended up using own-prepared 1000G phase 3 panel. Have a nice day!

Answer 1

[nielsoca]

I just ran into the same problem and then realized I had mistakenly entered my region of interest to be plotted in KB instead of MB. Easy fix!