IGV preferences

docs/run-notes/19373_run_notes.md

@@ -40,7 +40,32 @@ qsub -v SOURCE_DIR=${SOURCE_DIR}/${VERSION_N}_${BATCH_NUM},BATCH_ID=${BATCH_ID},
 
 ## IGV snapshots
 
-TODO
+`/home/u035/project/scripts/igv.prefs.properties`
+
+```
+SAM.SHADE_BASE_QUALITY=true
+SAM.GROUP_OPTION=SAMPLE
+SAM.DOWNSAMPLE_READS=false
+SAM.SORT_OPTION=STRAND
+SAM.COLOR_BY=READ_STRAND
+LAST_TRACK_DIRECTORY=/scratch/u035/project/trio_whole_exome/analysis/20211006_19373/DECIPHER/IGV
+DEFAULT_GENOME_KEY=hg38
+SAM.SHOW_CENTER_LINE=true
+
+##RNA
+SAM.SHADE_BASE_QUALITY=true
+SAM.SORT_OPTION=STRAND
+
+##THIRD_GEN
+SAM.SHADE_BASE_QUALITY=true
+SAM.SORT_OPTION=STRAND
+```
+
+```
+cd /scratch/u035/project/trio_whole_exome/analysis/20211006_19373/DECIPHER/IGV
+cat *.snapshot.FLT.txt > batch.snapshots.txt
+cat bamout_*.snapshot.txt > batch.bamout.snapshots.txt
+```
 
 # Shared affected analysis