Error BAM file(s) do not have the contig: hs37d5?

Question

[vctrm67]

I am running GATK Mutect using the b37 reference genome on some BAM files. However, I keep getting this error:

BAM file(s) do not have the contig: hs37d5. You are probably using a different reference than the one this file was aligned with

I double checked that the BAM files were created using b37 by looking at the header of the BAM files, so I'm not sure what's quite wrong:

@HD VN:1.4  GO:none SO:coordinate 
@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
@SQ SN:NC_007605    LN:171823

Does anyone know why I am getting this error?

Answer 1

[Pierre Lindenbaum]

I double checked that the BAM files were created using b37

yes, it's human b37 but it's not the same reference sequence. your reference sequence contains hs37d5 (decoy file) https://www.cureffi.org/2013/02/01/the-decoy-genome/

[vctrm67]

I see. Is there a place where I can download the non-decoy b37 reference?

[Ram]

It should be pretty straightforward to find online. Search for "hs37d5" and EMBL/NCBI should have the file.

[vctrm67]

Won't I get a file that includes hs37d5? Shouldn't I get a file that excludes hs37d5 so I don't get the same error?

[Ram]

Sorry, I misread the error. You can search for b37 - you'll find one of Heng Li's blog posts that will take you to a link on NCBI/EMBL/GENCODE. b37 should be easier to find than hs37d5.