Question: Extracted the chrM portion of bam into a new bam with header
gravatar for quachtina96
3.6 years ago by
United States
quachtina9620 wrote:

Hello,  I used 

samtools view -b -h exome.bam chrM > extractedchrM.bam

to extract the mitochondrial DNA from an exome into a bam file and to include a header. I was wondering if the header below was correct considering that my new bam is only chrM, but the header has more than that.  Is it because it just takes the header of the original bam file?

@HD     VN:1.4  SO:coordinate
@SQ     SN:chrM LN:16571
@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:chr1_gl000191_random LN:106433
@SQ     SN:chr1_gl000192_random LN:547496
@SQ     SN:chr4_ctg9_hap1       LN:590426
@SQ     SN:chr4_gl000193_random LN:189789
@SQ     SN:chr4_gl000194_random LN:191469
@SQ     SN:chr6_apd_hap1        LN:4622290
@SQ     SN:chr6_cox_hap2        LN:4795371
@SQ     SN:chr6_dbb_hap3        LN:4610396
@SQ     SN:chr6_mann_hap4       LN:4683263
@SQ     SN:chr6_mcf_hap5        LN:4833398
@SQ     SN:chr6_qbl_hap6        LN:4611984
@SQ     SN:chr6_ssto_hap7       LN:4928567
@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_ctg5_hap1      LN:1680828
@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
@RG     ID:ID18_Father_exome_L001       PL:ILLUMINA     PU:L001 LB:ID18_Father_exome    SM:ID18_Father_exome
bam chrm samtools header • 1.2k views
ADD COMMENTlink modified 3.6 years ago by Gabriel R.2.5k • written 3.6 years ago by quachtina9620
gravatar for Gabriel R.
3.6 years ago by
Gabriel R.2.5k
Center for Geogenetik Københavns Universitet
Gabriel R.2.5k wrote:

Yes, otherwise you would have to reassign a new Reference ID to every read.

ADD COMMENTlink written 3.6 years ago by Gabriel R.2.5k
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