IGV is not showing all alignments of SAM file

Question

[gernophil]

I manually created a SAM file:

GENE1_1 16  11  1185016 255 20M *   0   0   AGAACAACCTCTGCCTCTCC    *
GENE1_2 16  11  1185017 255 20M *   0   0   GAACAACCTCTGCCTCTCCA    *
GENE2_1 0   17  7673795 255 20M *   0   0   ACAAACACGCACCTCAAAGC    *
GENE2_2 0   17  7673796 255 20M *   0   0   CAAACACGCACCTCAAAGCT    *
GENE2_3 0   17  7673797 255 20M *   0   0   AAACACGCACCTCAAAGCTG    *
GENE2_4 0   17  7673798 255 20M *   0   0   AACACGCACCTCAAAGCTGT    *
GENE2_5 0   17  7673799 255 20M *   0   0   ACACGCACCTCAAAGCTGTT    *

If I load that into IGV the alignment of the read GENE2_1 is not shown. If I change the order of the reads to this:

GENE2_1 0   17  7673795 255 20M *   0   0   ACAAACACGCACCTCAAAGC    *
GENE2_2 0   17  7673796 255 20M *   0   0   CAAACACGCACCTCAAAGCT    *
GENE2_3 0   17  7673797 255 20M *   0   0   AAACACGCACCTCAAAGCTG    *
GENE2_4 0   17  7673798 255 20M *   0   0   AACACGCACCTCAAAGCTGT    *
GENE2_5 0   17  7673799 255 20M *   0   0   ACACGCACCTCAAAGCTGTT    *
GENE1_1 16  11  1185016 255 20M *   0   0   AGAACAACCTCTGCCTCTCC    *
GENE1_2 16  11  1185017 255 20M *   0   0   GAACAACCTCTGCCTCTCCA    *

IGV does show the alignment of the read GENE2_1, but now the alignment of GENE1_1 is not shown. What is happening here?

[GenoMax]

Alignments are downsampled according to their start position by default. You may need to turn off that option. It is somewhat buried in preferences.

[gernophil]

Unfortunately, that doesn't help

[Istvan Albert]

the downsampling will only happen for a large number of alignments,

for such a few number of alignments, all should be displayed

Answer 1

[Istvan Albert]

I verified this behavior, and I can observe the same oddity, which would I report as: the first alignment after switching chromosomes does not show up:

@SQ SN:11   LN:10000000
@SQ SN:17   LN:10000000
read1   16  11  1185016 255 20M *   0   0   AGAACAACCTCTGCCTCTCC    *
read2   0   17  7673795 255 20M *   0   0   ACAAACACGCACCTCAAAGC    *
read3   0   17  7673796 255 20M *   0   0   CAAACACGCACCTCAAAGCT    *

Notably, once the SAM file is sorted and converted to BAM, the alignments do show up.

Converting back from BAM to SAM into a new SAM file IGV again fails to display the alignment for read2.

I think it is a bug.

Solution: convert to BAM format.

[GenoMax]

So it would be best for OP to report it via IGV help channel: https://groups.google.com/g/igv-help

[gernophil]

Thanks for all your efforts. I will report this tomorrow and use BAM files for now :).