I can not see BAM file in IGV
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
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I tried sorting and then indexing and now it is working
samtools sort A.bam -o B.bam
samtools index B.bam
Thanks
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what's the version of IGV. What is the region (chr-start-end) your trying to zoom-in ?
The version is I.G.V_2.3.93 I have tried chr10:65,266,569-65,287,741
what is the output of
Please post the full backtrace that IGV reports. My guess is that there's an issue with the BAM index, so maybe reindex it.