SAM Tracks Are Missing Reads

[Dario Strbenac]

I have a file which I indexed as a SAM file, then also converted it into BAM and indexed that. The SAM file only shows the first read per contig (i.e. SAM track read ID identical to BAM track left-most read) whereas the BAM track shows all mapped reads. I think there's a bug in the SAM file rendering. I used version 2.3.92 of IGV.