What is the best method to use IGV to view structural mutations？

[user-tq]

This is a great tool. But the usage instructions related to structural variation seem to be lacking, which makes me a bit confused. I need to visualize bam file（illunima PE）. I chose group by alignment pair orientation,and Through the screen splitting method here, i chose View mate region in split screen .

Of course, this is consistent with the results I obtained from delly's bcf.

2   29448234    INV00000097 A   <INV>   10000   PASS    PRECISE;SVTYPE=INV;SVMETHOD=EMBL.DELLYv1.1.6;END=29448692;PE=345;MAPQ=60;CT=3to3;CIPOS=-4,4;CIEND=-4,4;SRMAPQ=60;INSLEN=0;HOMLEN=3;SR=20;SRQ=1;CONSENSUS=AATCAGGGGCTCCTCAGGGAACTGCAGCTGCTCTGGTGGGGGGAAGGTTGGGAGCTTCCGTTTTGGCTTGGCCTGGGCTGCCCTAATCACCACCCCACCCAATTCCAGGGACTAGCATAACGAATGTTTCAAACCAACATCCCGCCACTGATATTCATCC;CE=1.9883 GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/1:-153.834,0,-420.992:10000:PASS:1330534:2579570:993231:2:2340:347:170:80
2   29448310    DUP00000099 G   <DUP>   1200    PASS    PRECISE;SVTYPE=DUP;SVMETHOD=EMBL.DELLYv1.1.6;END=42507520;PE=0;MAPQ=0;CT=5to3;CIPOS=-2,2;CIEND=-2,2;SRMAPQ=60;INSLEN=0;HOMLEN=2;SR=20;SRQ=0.994792;CONSENSUS=TAAGGAAATGGCCATTGGTTTATTTTTCCCTACAATGTTTTAGACTAGGACTTTATAGTATCACTTTGTATTCGGGCTCTGTGCACTCACCAATCATGATGCCGGAGAAAGCCAGGACCAGGGCGGCCACGAGGGCAGAGGTCACCACAGAGAGGATCAGCGAGAGTGGCAGGTGTGGCTCCGGGGTGGGTG;CE=1.98362    GT:GL:GQ:FT:RCL:RC:RCR:RDCN:DR:DV:RR:RV 0/0:0,-75.1503,-755.993:10000:PASS:191585:102194:98208:1:0:0:250:0

This makes me a bit confused, there are too few reads on the left screen. Is it due to downsampling?How many reads does this variant be supported? I wonder if there's anything like 'View split reads in split screen', This seems more conducive to finding breakpoints Of course, Delly's results also surprised me,(the RV=0). Thank you for any advice

[jrobinso]

The reads on the left are definitely downsampled, you can tell by the black bars under the coverage graph. See the user guide for details on downsampling. There is a "view split reads in split screen" in the development build, which will be released by the end of September. If you would like to try it before then you can use the snapshot build: https://software.broadinstitute.org/software/igv/download_snapshot