I can not see BAM file in IGV

Question

[Michel Edwar]

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

[Devon Ryan]

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

[Pierre Lindenbaum]

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

[Michel Edwar]

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

[Pierre Lindenbaum]

what is the output of

samtools view -c your.bam "chr10:65266569-65287741"

Answer 1

[Michel Edwar]

I tried sorting and then indexing and now it is working

samtools sort A.bam -o B.bam
samtools index  B.bam

Thanks