Question: IGV genome browser not displaying visualization when BAM file is uploaded
gravatar for tw617
22 months ago by
tw61740 wrote:

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
igv alignment • 549 views
ADD COMMENTlink modified 22 months ago by GenoMax94k • written 22 months ago by tw61740

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.

ADD REPLYlink modified 22 months ago • written 22 months ago by GenoMax94k

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

ADD REPLYlink written 22 months ago by tw61740
gravatar for Devon Ryan
22 months ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

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.

ADD COMMENTlink written 22 months ago by Devon Ryan98k

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

ADD REPLYlink modified 22 months ago • written 22 months ago by tw61740
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