Question: Locus Zoom issues no error but prints file with no LD information displayed
1
gravatar for Vincent Laufer
2.2 years ago by
Vincent Laufer1.0k
United States
Vincent Laufer1.0k wrote:

I am attempting to use the --ld option on LocusZoom (please see here: http://genome.sph.umich.edu/wiki/LocusZoom_Standalone ). I have contacted the authors several times and never received a response, so I would like to ask the community if you have ever submitted a query of the form:

$LOCUSZOOM --epacts $INFILEDIR/$INFILE \
--ld $INFILEDIR/$LINKAGE_FILE \
--ld-measure rsquare \
--chr $CHR --start $STARTPOS --end $ENDPOS

and received a plot with the dots colored appropriately. In response to the above command, locuszoom will print a pdf with all the dots colored grey but will not issue an error. The output is below:

bash locuszoomtester_empirical_ld.sh 
+---------------------------------------------+
| LocusZoom 1.3 (06/20/2014)                  |
| Plot regional association results           |
| from GWA scans or candidate gene studies    |
+---------------------------------------------+

Loading settings..
Options in effect are:

+------------+------------------------------------------------------------------------------+
|   Option   |                                    Value                                     |
+------------+------------------------------------------------------------------------------+
| epacts     | ICHIP_ZINB_SQRTDD_FOR_LZ_COUNT.txt                                           |
| chr        | 10                                                                           |
| start      | 6000000                                                                      |
| end        | 6200000                                                                      |
| build      | hg18                                                                         |
| ld         | new_linkage_file_il2ra.txt |
| ld-measure | rsquare                                                                      |
| pop        | CEU                                                                          |
| source     | hapmap                                                                       |
| snpset     | Illu1M                                                                       |
| gene-table | refFlat                                                                      |
| cache      | ../ld_cache.db                                                               |
+------------+------------------------------------------------------------------------------+

Plotting parameters in effect are:

+-----------+------------+
|   Option  |   Value    |
+-----------+------------+
| markerCol | MarkerName |
| pvalCol   | P-value    |
+-----------+------------+

Using /tools/locuszoom/bin/locuszoom.R..
Beginning plotting sequence for: chr10_6000000-6200000
Extracting region of interest (chr10:6000000-6200000) from input file..
Attempting to find best SNP in region..
Found: chr10:6132692 
Using user-specified LD file..
Grabbing annotations from SQLite database..
Creating plot..
Deleting temporary files..
Time required: 0d:0h:0m:3s

To me, it looks like it processes the commands, but then also still reverts back to CEU for some reason (it has a pop CEU entry despite no input to that effect).

What am I doing wrong?

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Vincent Laufer1.0k
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