Question: I can not see BAM file in IGV

0

Michel Edwar •

**70**wrote:I have uploaded a bam file with index into IGV and I only see the reference gene but not my actual bam file. when i try to zoom in , I get this error message.

Error encountered querying alignments: java.lang.IllegalArgumentException: Size exceeds Integer.MAX_VALUE

I have tried using sam tools to view the file and I got

```
@HD VN:1.0 SO:coordinate
@SQ SN:chr10 LN:130694993
@SQ SN:chr11 LN:122082543
@SQ SN:chr12 LN:120129022
@SQ SN:chr13 LN:120421639
@SQ SN:chr14 LN:124902244
@SQ SN:chr15 LN:104043685
@SQ SN:chr16 LN:98207768
@SQ SN:chr17 LN:94987271
@SQ SN:chr18 LN:90702639
@SQ SN:chr19 LN:61431566
@SQ SN:chr1 LN:195471971
@SQ SN:chr2 LN:182113224
@SQ SN:chr3 LN:160039680
@SQ SN:chr4 LN:156508116
@SQ SN:chr5 LN:151834684
@SQ SN:chr6 LN:149736546
@SQ SN:chr7 LN:145441459
@SQ SN:chr8 LN:129401213
@SQ SN:chr9 LN:124595110
@SQ SN:chrM LN:16299
@SQ SN:chrX LN:171031299
@SQ SN:chrY LN:91744698
@PG ID:bowtie2 PN:bowtie2 VN:2.0.2
SN7001140:278:CA46MACXX:6:2302:17112:37665 0 chr10 3100065 1 50M * ATCATCAGGGAAATGCAAATCAAAACAACACTGAGATTCCACTTCACTCC BBBFFFFFFFFFFIIIIIIIIIIIIIFIIFIIFIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU
SN7001140:278:CA46MACXX:6:1105:18571:34597 0 chr10 3100065 1 50M * ATCATCAGGGAAATGCAAATCAAAACAACACTGAGATTCCACTTCACTCC BBBFFFFFFFFFFIIIFFIIIIIIIIIIIBFIIIIIIIIIIIIIIFIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU
SN7001140:278:CA46MACXX:6:2311:5844:19263 16 chr10 3100085 1 50M * CAAAACAACACTGAGATTCCACTTCACTCCAGTTAGAATGGCTAAGATCA IIIFFFFBBFIIIIIIIIIIFIFFFBIIIIIIIIIIIFFFFFFFFFFBBB AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU
SN7001140:278:CA46MACXX:6:2212:11695:72194 16 chr10 3100220 1 50M * ACCACTCTGGAAATCAGTCTGGCGGTTCCTCAGAAAATTGGACATAGTAC 7FFBFFFBIIIIFFFFIIFFIIIIIFFFFFIIIIFFFFFFFFFFFFFBBB AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU
SN7001140:278:CA46MACXX:6:2203:11295:88236 16 chr10 3100220 1 50M * ACCACTCTGGAAATCAGTCTGGCGGTTCCTCAGAAAATTGGACATAGTAC FFFBFBIIIIIIIFIIIIIIIIIIIIIFFFIIIIIFIFFFFFBFFFFBBB AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU
SN7001140:278:CA46MACXX:6:2207:2637:5372 16 chr10 3100220 1 50M * ACCACTCTGGAAATCAGTCTGGCGGTTCCTCAGAAAATTGGACATAGTAC FIFFIIIIIIIIIIIIIIIIIIIIFIIIIIIIIIIIIFFFFFFFFFFBBB AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU
```

Please post the full backtrace that IGV reports. My guess is that there's an issue with the BAM index, so maybe reindex it.

96kwhat's the version of IGV. What is the region (chr-start-end) your trying to zoom-in ?

129kThe version is I.G.V_2.3.93 I have tried chr10:65,266,569-65,287,741

70what is the output of

129k