Hg19 version based on bam file contigs?

Question

[vctrm67]

Does anyone know which version of hg19 this is based on the sequence contigs in the bam file header?

@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr5 LN:180915260
@SQ SN:chr6 LN:171115067
@SQ SN:chr7 LN:159138663
@SQ SN:chr8 LN:146364022
@SQ SN:chr9 LN:141213431
@SQ SN:chr10    LN:135534747
@SQ SN:chr11    LN:135006516
@SQ SN:chr12    LN:133851895
@SQ SN:chr13    LN:115169878
@SQ SN:chr14    LN:107349540
@SQ SN:chr15    LN:102531392
@SQ SN:chr16    LN:90354753
@SQ SN:chr17    LN:81195210
@SQ SN:chr18    LN:78077248
@SQ SN:chr19    LN:59128983
@SQ SN:chr20    LN:63025520
@SQ SN:chr21    LN:48129895
@SQ SN:chr22    LN:51304566
@SQ SN:chrX LN:155270560
@SQ SN:chrY LN:59373566
@SQ SN:chrM LN:16571
@SQ SN:chr1_gl000191_random LN:106433
@SQ SN:chr1_gl000192_random LN:547496
@SQ SN:chr4_gl000193_random LN:189789
@SQ SN:chr4_gl000194_random LN:191469
@SQ SN:chr7_gl000195_random LN:182896
@SQ SN:chr8_gl000196_random LN:38914
@SQ SN:chr8_gl000197_random LN:37175
@SQ SN:chr9_gl000198_random LN:90085
@SQ SN:chr9_gl000199_random LN:169874
@SQ SN:chr9_gl000200_random LN:187035
@SQ SN:chr9_gl000201_random LN:36148
@SQ SN:chr11_gl000202_random    LN:40103
@SQ SN:chr17_gl000203_random    LN:37498
@SQ SN:chr17_gl000204_random    LN:81310
@SQ SN:chr17_gl000205_random    LN:174588
@SQ SN:chr17_gl000206_random    LN:41001
@SQ SN:chr18_gl000207_random    LN:4262
@SQ SN:chr19_gl000208_random    LN:92689
@SQ SN:chr19_gl000209_random    LN:159169
@SQ SN:chr21_gl000210_random    LN:27682
@SQ SN:chrUn_gl000211   LN:166566
@SQ SN:chrUn_gl000212   LN:186858
@SQ SN:chrUn_gl000213   LN:164239
@SQ SN:chrUn_gl000214   LN:137718
@SQ SN:chrUn_gl000215   LN:172545
@SQ SN:chrUn_gl000216   LN:172294
@SQ SN:chrUn_gl000217   LN:172149
@SQ SN:chrUn_gl000218   LN:161147
@SQ SN:chrUn_gl000219   LN:179198
@SQ SN:chrUn_gl000220   LN:161802
@SQ SN:chrUn_gl000221   LN:155397
@SQ SN:chrUn_gl000222   LN:186861
@SQ SN:chrUn_gl000223   LN:180455
@SQ SN:chrUn_gl000224   LN:179693
@SQ SN:chrUn_gl000225   LN:211173
@SQ SN:chrUn_gl000226   LN:15008
@SQ SN:chrUn_gl000227   LN:128374
@SQ SN:chrUn_gl000228   LN:129120
@SQ SN:chrUn_gl000229   LN:19913
@SQ SN:chrUn_gl000230   LN:43691
@SQ SN:chrUn_gl000231   LN:27386
@SQ SN:chrUn_gl000232   LN:40652
@SQ SN:chrUn_gl000233   LN:45941
@SQ SN:chrUn_gl000234   LN:40531
@SQ SN:chrUn_gl000235   LN:34474
@SQ SN:chrUn_gl000236   LN:41934
@SQ SN:chrUn_gl000237   LN:45867
@SQ SN:chrUn_gl000238   LN:39939
@SQ SN:chrUn_gl000239   LN:33824
@SQ SN:chrUn_gl000240   LN:41933
@SQ SN:chrUn_gl000241   LN:42152
@SQ SN:chrUn_gl000242   LN:43523
@SQ SN:chrUn_gl000243   LN:43341
@SQ SN:chrUn_gl000244   LN:39929
@SQ SN:chrUn_gl000245   LN:36651
@SQ SN:chrUn_gl000246   LN:38154
@SQ SN:chrUn_gl000247   LN:36422
@SQ SN:chrUn_gl000248   LN:39786
@SQ SN:chrUn_gl000249   LN:38502

I tried looking it up but couldn't find anything, especially a version of hg19 with chrM added. I found this but it contains more contigs than are shown here (84).

[GenoMax]

There should be only one version of hg19. There are patch releases that occur over time but they do not result in chromosome co-ordinate changes.

[vctrm67]

Oh. Do you know if this is hg19 then? I tried running some GATK tools but I get an error message that looks like:

##### ERROR MESSAGE: Input files reads and reference have incompatible contigs. Please see http://gatkforums.broadinstitute.org/discussion/63/input-files-have-incompatible-contigsfor more information. Error details: The contig order in reads and reference is not the same; to fix this please see: (https://www.broadinstitute.org/gatk/guide/article?id=1328),  which describes reordering contigs in BAM and VCF files..
##### ERROR   reads contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY, chrM, chr1_gl000191_random, chr1_gl000192_random, chr4_gl000193_random, chr4_gl000194_random, chr7_gl000195_random, chr8_gl000196_random, chr8_gl000197_random, chr9_gl000198_random, chr9_gl000199_random, chr9_gl000200_random, chr9_gl000201_random, chr11_gl000202_random, chr17_gl000203_random, chr17_gl000204_random, chr17_gl000205_random, chr17_gl000206_random, chr18_gl000207_random, chr19_gl000208_random, chr19_gl000209_random, chr21_gl000210_random, chrUn_gl000211, chrUn_gl000212, chrUn_gl000213, chrUn_gl000214, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chrUn_gl000218, chrUn_gl000219, chrUn_gl000220, chrUn_gl000221, chrUn_gl000222, chrUn_gl000223, chrUn_gl000224, chrUn_gl000225, chrUn_gl000226, chrUn_gl000227, chrUn_gl000228, chrUn_gl000229, chrUn_gl000230, chrUn_gl000231, chrUn_gl000232, chrUn_gl000233, chrUn_gl000234, chrUn_gl000235, chrUn_gl000236, chrUn_gl000237, chrUn_gl000238, chrUn_gl000239, chrUn_gl000240, chrUn_gl000241, chrUn_gl000242, chrUn_gl000243, chrUn_gl000244, chrUn_gl000245, chrUn_gl000246, chrUn_gl000247, chrUn_gl000248, chrUn_gl000249]
##### ERROR   reference contigs = [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chrX, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr20, chrY, chr19, chr22, chr21, chr6_ssto_hap7, chr6_mcf_hap5, chr6_cox_hap2, chr6_mann_hap4, chr6_apd_hap1, chr6_qbl_hap6, chr6_dbb_hap3, chr17_ctg5_hap1, chr4_ctg9_hap1, chr1_gl000192_random, chrUn_gl000225, chr4_gl000194_random, chr4_gl000193_random, chr9_gl000200_random, chrUn_gl000222, chrUn_gl000212, chr7_gl000195_random, chrUn_gl000223, chrUn_gl000224, chrUn_gl000219, chr17_gl000205_random, chrUn_gl000215, chrUn_gl000216, chrUn_gl000217, chr9_gl000199_random, chrUn_gl000211, chrUn_gl000213, chrUn_gl000220, chrUn_gl000218, chr19_gl000209_random, chrUn_gl000221, chrUn_gl000214, chrUn_gl000228, chrUn_gl000227, chr1_gl000191_random, chr19_gl000208_random, chr9_gl000198_random, chr17_gl000204_random, chrUn_gl000233, chrUn_gl000237, chrUn_gl000230, chrUn_gl000242, chrUn_gl000243, chrUn_gl000241, chrUn_gl000236, chrUn_gl000240, chr17_gl000206_random, chrUn_gl000232, chrUn_gl000234, chr11_gl000202_random, chrUn_gl000238, chrUn_gl000244, chrUn_gl000248, chr8_gl000196_random, chrUn_gl000249, chrUn_gl000246, chr17_gl000203_random, chr8_gl000197_random, chrUn_gl000245, chrUn_gl000247, chr9_gl000201_random, chrUn_gl000235, chrUn_gl000239, chr21_gl000210_random, chrUn_gl000231, chrUn_gl000229, chrM, chrUn_gl000226, chr18_gl000207_random]

Answer 1

[GenoMax]

Check this answer from a while back: A: Additional Data In Human Genome (Hg18 / Hg19) Assembly ? Looks like your reference has alternate MHC haplotypes.

There is also this complication: Are There Different Versions For The Human Mt Contig B37? I See A 2Bp Difference In Length

[vctrm67]

I think my problem has more so to do with that the reference hg19 includes contigs beyond the unmapped sequences that aren't reflected in what the BAM file is aligned with. As you can see, the list of contigs for the reference is longer than the list of contigs for the reads.

[GenoMax]

Not sure what exactly you are saying. As long as your reference is a superset of what your BAM was aligned to, it should cover the reference that you actually used.

BTW: Did you also check the link that is in the error message above?