Error BAM file(s) do not have the contig: hs37d5?
1
0
Entering edit mode
19 months ago
vctrm67 ▴ 20

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?

software error • 639 views
ADD COMMENT
0
Entering edit mode
19 months ago

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/

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2380 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6