IGV pileup not showing any reads at any position in bam

Question

[bioguy24]

I am not able to figure out why when I load an Ion Torrent bam file into IGV the result is a blank/empty pileup. I routinely run these bam files and have no problems, but am now and not sure why. This is a bam uses a hotspot file, but I am not sure if that is necessary or how to load it properly.

 samtools view -h torrent_316.2017_A.bam | head -20

 @HD    VN:1.4  GO:none SO:coordinate
 @SQ    SN:chr1 LN:249250621
 @SQ    SN:chr2 LN:243199373
 @SQ    SN:chr3 LN:198022430
 @SQ    SN:chr4 LN:191154276
 @SQ    SN:chr5 LN:180915260
 @SQ    SN:chr6 LN:171115067
 @SQ    SN:chr7 LN:159138663
 @SQ    SN:chr8 LN:146364022
 @SQ    SN:chr9 LN:141213431
 @SQ    SN:chr10    LN:135534747
 @SQ    SN:chr11    LN:135006516
 @SQ    SN:chr12    LN:133851895
 @SQ    SN:chr13    LN:115169878
 @SQ    SN:chr14    LN:107349540
 @SQ    SN:chr15    LN:102531392
 @SQ    SN:chr16    LN:90354753
 @SQ    SN:chr17    LN:81195210
 @SQ    SN:chr18    LN:78077248
 @SQ    SN:chr19    LN:59128983
 @SQ    SN:chr20    LN:63025520
 @SQ    SN:chr21    LN:48129895
 @SQ    SN:chr22    LN:51304566
 @SQ    SN:chrX LN:155270560
 @SQ    SN:chrY LN:59373566
 @SQ    SN:chrM LN:16569
 @RG    ID:PP5M3.IonXpress_002  PL:IONTORRENT   PU:PGM/316v2/IonXpress_002  LB:hg19/IonXpress_002   FO:TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCA DT:2014-10-10T17:17:22-0500 SM:NGS_02_CAP_316   PG:tmap KS:TCAGTAAGGAGAACGAT    CN:TorrentServer/sn274670099

Also, the result of this command shows zero reads at this position:

 samtools view -c torrent_316.2017_A.bam "chr1:115258747"
 0

However, the variant caller in Ion Reporter called a SNV with 1935 reads.

Thank you :).

[Istvan Albert]

Run a flagstat on this not just an intersection of a single coordinate.