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?