#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