#new
#setSleepInterval 200

genome hg19


# load annotation tracks
# Obtained the URLs by loading the annotation track in IGV (File> Load
# from Server), saved the session and opened the .xml file in a text editor to get the URLs
#load Ensembl gene, dbsnp, DGV, GC content, 
load http://www.broadinstitute.org/igvdata/annotations/hg19/EnsemblGenes.ensGene,https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/snp147.hg19.ucscsnp.gz,https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/dgv.bed.gz,http://www.broadinstitute.org/igvdata/annotations/hg19/hg19.gc5base.tdf

#**** change these paths to point to your files:
# load bam file
load /Users/florence/Canadian_Bioinfo_workshop/CHSHL_March2017/CHSHL_March_workshop/Module2/HCC1143.normal.21.19M-20M.bam,/Users/florence/Canadian_Bioinfo_workshop/CHSHL_March2017/CHSHL_March_workshop/Module2/igv_HCC1143_attributes.txt


# **** change this path to your output directory 
snapshotDirectory /Users/florence/Canadian_Bioinfo_workshop/CHSHL_March2017/CHSHL_March_workshop/Module2/igv/screenshots/


# Example1:
goto chr21:19,479,731-19,479,731
sort base chr21:19,479,731
maxPanelHeight 50000
snapshot HCC1143_exercise1_SNV_SNP_pair.png

# Example2:
goto chr21:19,518,452-19,518,452
sort base chr21:19,518,452
snapshot HCC1143_exercise2_homopolymerRepeat.png

# Example3:
goto chr21:19,611,925-19,631,555
collapse
snapshot HCC1143_exercise3_lowGC.png

# Example4:
goto chr21:19,666,890-19,666,930
expand
sort base
snapshot HCC1143_exercise4_hetSNP_allelic.png


# Example6:
goto chr21:19,324,469-19,331,468
expand
viewaspairs
snapshot HCC1143_exercise6_homDEL.png

# Example7:
goto chr21:19,102,154-19,103,108
snapshot HCC1143_exercise7_AluY.png

# Example8:
goto chr21:19,089,694-19,095,362
expand
snapshot HCC1143_exercise8_translocation.png


# Example5:
# load LINE element track
load https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg19/variations/LINE.rmask.gz
goto chr21:19,800,320-19,818,162
collapse
snapshot HCC1143_exercise5_LINErepeat.png

# exit