View As Pairs somewhat counter-intuitive behavior - better documentation needed?

[Malcolm Cook]

Hi,

I find that when I load a track containing paired end reads, if I am zoomed in to a region that holds only one read of a mate pair, and then turn on "View As Pairs", IGV will not display a line coming out of the read to show that it is has a mate pair.   

However, IGV knows it has a mate pair.  For example, If I turn on grouping/coloring by pair-orientation, the read is correctly color coded.

Now, if I zoom out to the region holding the first read AND its mate, only at that time is a line drawn joining the reads.

Furthermore, if I zoom back to the original location, the line is preserved.

For example, if I load a .bam file holding in the mate-pair documented below, and I am zoomed into the locus holding the Left side (i.e. ScGoXVd_1602:10,504,196-10,504,499 is the read +/- 100bp) IGV draws no line.

When I zoom out to the region holding both alignments +/- 100bp, being ScGoXVd_1602:10,504,296-10,557,476 I now see the line.

Finally, if I zoom back into ScGoXVd_1602:10,504,196-10,504,499 the line persists.

I'm not sure what IGV should do, but it took me a while to appreciate what it does do.   

Jim, if this is operating as designed, perhaps it could be documented better in http://www.broadinstitute.org/software/igv/AlignmentData#paired where it currently reads                      "Select View as pairs from the right-click menu to display pairs together with a line joining the ends as shown in the image below"

It might additionally say  

              "Lines are only drawn when both members of the pair are on-screen, or have been on screen, and are still in JAVA's heap" (or something, whatever it is).

There have been a few unresolved posts on this forum that may possibly be explained with this understanding.

    https://groups.google.com/d/msg/igv-help/hU4RdwyRe5g/18Fg_C-bAJUJ

    https://groups.google.com/d/msg/igv-help/2yGiaIXz5nc/LencIsbo75QJ

~Malcolm

Left alignment Read name = SN639:758:HJTYHBCXX:2:1211:13395:43416 Sample = sm Read group = FASTQ ---------------------- Location = ScGoXVd_1602:10,504,399 Alignment start = 10,504,296 (-) Cigar = 151M Mapped = yes Mapping quality = 70 Secondary = no Supplementary = no Duplicate = no Failed QC = no ---------------------- Base = G Base phred quality = 38 ---------------------- Mate is mapped = yes Mate start = ScGoXVd_1602:10557375 (-) Insert size = 52928 Second in pair Pair orientation = R2R1 ---------------------- LB = lb PG = SNAP RG = FASTQ PL = Illumina NM = 0 SM = sm MQ = 26 PU = pu xj = T xs = 35 xt = D -------------------

Right alignment Read name = SN639:758:HJTYHBCXX:2:1211:13395:43416 Sample = sm Read group = FASTQ ---------------------- Location = ScGoXVd_1602:10,504,399 Alignment start = 10,557,376 (-) Cigar = 116S35M Mapped = yes Mapping quality = 26 Secondary = no Supplementary = no Duplicate = no Failed QC = no ---------------------- ---------------------- Mate is mapped = yes Mate start = ScGoXVd_1602:10504295 (-) Insert size = 53044 First in pair Pair orientation = R1R2 ---------------------- LB = lb PG = SNAP RG = FASTQ PL = Illumina NM = 0 SM = sm MQ = 70 PU = pu xj = T xs = 151 xt = D -------------------

[Jim Robinson]

This would make a good git issue.

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[Malcolm Cook]

done:  https://github.com/igvteam/igv/issues/260