IGV genome browser not displaying visualization when BAM file is uploaded

Question

[tw617]

Hi, I have a BAM file that I am trying to visualize against the hg19 genome in IGV. I created an index for the file and hg19 is loaded in IGV. When I drag and drop the file there is nothing displayed. It seems like I may have to create an alias file, but the chromosome names in the bam file seem like they should be covered by the default IGV settings. What should I do?

This is the header of my BAM file:

$ samtools view -H subset.bam
@HD     VN:1.0  SO:coordinate   GO:none
@SQ     SN:1    LN:249250621
@SQ     SN:2    LN:243199373
@SQ     SN:3    LN:198022430
@SQ     SN:4    LN:191154276
@SQ     SN:5    LN:180915260
@SQ     SN:6    LN:171115067
@SQ     SN:7    LN:159138663
@SQ     SN:8    LN:146364022
@SQ     SN:9    LN:141213431
@SQ     SN:10   LN:135534747
@SQ     SN:11   LN:135006516
@SQ     SN:12   LN:133851895
@SQ     SN:13   LN:115169878
@SQ     SN:14   LN:107349540
@SQ     SN:15   LN:102531392
@SQ     SN:16   LN:90354753
@SQ     SN:17   LN:81195210
@SQ     SN:18   LN:78077248
@SQ     SN:19   LN:59128983
@SQ     SN:20   LN:63025520
@SQ     SN:21   LN:48129895
@SQ     SN:22   LN:51304566
@SQ     SN:X    LN:155270560
@SQ     SN:Y    LN:59373566
@SQ     SN:MT   LN:16569
@SQ     SN:GL000207.1   LN:4262
@SQ     SN:GL000226.1   LN:15008
@SQ     SN:GL000229.1   LN:19913
@SQ     SN:GL000231.1   LN:27386
@SQ     SN:GL000210.1   LN:27682
@SQ     SN:GL000239.1   LN:33824
@SQ     SN:GL000235.1   LN:34474
@SQ     SN:GL000201.1   LN:36148
@SQ     SN:GL000247.1   LN:36422
@SQ     SN:GL000245.1   LN:36651
@SQ     SN:GL000197.1   LN:37175
@SQ     SN:GL000203.1   LN:37498
@SQ     SN:GL000246.1   LN:38154
@SQ     SN:GL000249.1   LN:38502
@SQ     SN:GL000196.1   LN:38914
@SQ     SN:GL000248.1   LN:39786
@SQ     SN:GL000244.1   LN:39929
@SQ     SN:GL000238.1   LN:39939
@SQ     SN:GL000202.1   LN:40103
@SQ     SN:GL000234.1   LN:40531
@SQ     SN:GL000232.1   LN:40652
@SQ     SN:GL000206.1   LN:41001
@SQ     SN:GL000240.1   LN:41933
@SQ     SN:GL000236.1   LN:41934
@SQ     SN:GL000241.1   LN:42152
@SQ     SN:GL000243.1   LN:43341
@SQ     SN:GL000242.1   LN:43523
@SQ     SN:GL000230.1   LN:43691
@SQ     SN:GL000237.1   LN:45867
@SQ     SN:GL000233.1   LN:45941
@SQ     SN:GL000204.1   LN:81310
@SQ     SN:GL000198.1   LN:90085
@SQ     SN:GL000208.1   LN:92689
@SQ     SN:GL000191.1   LN:106433
@SQ     SN:GL000227.1   LN:128374
@SQ     SN:GL000228.1   LN:129120
@SQ     SN:GL000214.1   LN:137718
@SQ     SN:GL000221.1   LN:155397
@SQ     SN:GL000209.1   LN:159169
@SQ     SN:GL000218.1   LN:161147
@SQ     SN:GL000220.1   LN:161802
@SQ     SN:GL000213.1   LN:164239
@SQ     SN:GL000211.1   LN:166566
@SQ     SN:GL000199.1   LN:169874
@SQ     SN:GL000217.1   LN:172149
@SQ     SN:GL000216.1   LN:172294
@SQ     SN:GL000215.1   LN:172545
@SQ     SN:GL000205.1   LN:174588
@SQ     SN:GL000219.1   LN:179198
@SQ     SN:GL000224.1   LN:179693
@SQ     SN:GL000223.1   LN:180455
@SQ     SN:GL000195.1   LN:182896
@SQ     SN:GL000212.1   LN:186858
@SQ     SN:GL000222.1   LN:186861
@SQ     SN:GL000200.1   LN:187035
@SQ     SN:GL000193.1   LN:189789
@SQ     SN:GL000194.1   LN:191469
@SQ     SN:GL000225.1   LN:211173
@SQ     SN:GL000192.1   LN:547496
@RG     ID:B1087        SM:DenisovaPinky        LB:97_1 PL:Illumina
@RG     ID:B1088        SM:DenisovaPinky        LB:104_2        PL:Illumina
@RG     ID:B1101        SM:DenisovaPinky        LB:98_6 PL:Illumina
@RG     ID:B1102        SM:DenisovaPinky        LB:106_7        PL:Illumina
@RG     ID:B1107        SM:DenisovaPinky        LB:97_1 PL:Illumina
@RG     ID:B1108        SM:DenisovaPinky        LB:104_2        PL:Illumina
@RG     ID:B1109        SM:DenisovaPinky        LB:98_6 PL:Illumina
@RG     ID:B1110        SM:DenisovaPinky        LB:106_7        PL:Illumina
@RG     ID:B1128        SM:DenisovaPinky        LB:113_18       PL:Illumina
@RG     ID:B1130        SM:DenisovaPinky        LB:113_18       PL:Illumina
@RG     ID:B1133        SM:DenisovaPinky        LB:105_12       PL:Illumina
@RG     ID:SL3003       SM:DenisovaPinky        LB:SL3003       PL:Illumina
@RG     ID:SL3004       SM:DenisovaPinky        LB:SL3004       PL:Illumina
@PG     ID:GATK IndelRealigner  VN:1.3-17-gc62082b      CL:knownAlleles=[] LODThresholdForCleaning=5.0 consensusDeterminationModel=USE_READS entropyThreshold=0.15 maxReadsInMemory=150000 maxIsizeForMovement=3000 maxPositionalMoveAllowed=200 maxConsensuses=30 maxReadsForConsensuses=120 maxReadsForRealignment=20000 noOriginalAlignmentTags=false nWayOut=null generate_nWayOut_md5s=false check_early=false noPGTag=false keepPGTags=false indelsFileForDebugging=null statisticsFileForDebugging=null SNPsFileForDebugging=null

[GenoMax]

Have you tried to zoom in to a specific area? By default IGV does not show alignments unless you zoom in sufficiently. Type a gene of interest in the gene name search box and then dive in.

[tw617]

Yes, I tried zooming in and there is nothing there.

Answer 1

[Devon Ryan]

Are you sure there are alignments in the region you're looking at? Use samtools view to ensure there are reads in that particular region.

[tw617]

Ah.... I've figured it out. Thank you for pointing me in the right direction. I only downloaded reads on chromosome 3.