Dear Mr.samtools,
I'm Jiessie, a bioinformatic beginner from China, very sorry to disturb you!
I've used the "samtools reheader " command to replace the header of my bam
files, but the output file showed a small error as follows:
[my command] : samtools reheader new.header.sam s1_chr22.bam >
reheader.s1_chr22.bam
[the original header of bam file]:
@HD VN:1.0
@SQ SN:chr22 LN:51304566
@PG ID:segemehl VN:0.1.7-$Rev: 411 $ ($Date: 2014-06-18 ...
[the content of new.head.sam]:
@HD VN:1.0
@SQ SN:chr1 LN:249250621
@SQ SN:chr2 LN:243199373
@SQ SN:chr3 LN:198022430
@SQ SN:chr4 LN:191154276
@SQ SN:chr22 LN:51304566
@PG ID:segemehl VN:0.1.7-$Rev: 411 $ ($Date: 2014-06-18 ...
[the original bam file (brief view)]:
HWI-ST1269:287:H9BA4ADXX:1:1101:3481:1993 1:N:0 99 chr22 22890685 255 99M =
22890824 233 NGGGGG
HWI-ST1269:287:H9BA4ADXX:1:1101:3481:1993 2:N:0 147 chr22 22890824 255 94M =
22890685 -233 GGAGGG
HWI-ST1269:287:H9BA4ADXX:1:1101:3516:1883 2:N:0 145 chr22 29695606 255 94M * 0
0 GGTGGCCCTGGTGG
HWI-ST1269:287:H9BA4ADXX:1:1101:3516:1883 1:N:0 321 chr22 29694857 255 29M * 0
0 CGAGCTGGAGACTG
HWI-ST1269:287:H9BA4ADXX:1:1101:3516:1883 1:N:0 321 chr22 29695224 255 69M * 0
0 GGGTTGTGGAAACC
HWI-ST1269:287:H9BA4ADXX:1:1101:3778:1975 1:N:0 83 chr22 29678425 255 99M =
29674081 -4250
[bam file after replacing its header(brief view)]:
HWI-ST1269:287:H9BA4ADXX:1:1101:3481:1993 1:N:0 99 chr1 22890685 255 99M =
22890824 233 NGGGGG
HWI-ST1269:287:H9BA4ADXX:1:1101:3481:1993 2:N:0 147 chr1 22890824 255 94M =
22890685 -233 GGAGGG
HWI-ST1269:287:H9BA4ADXX:1:1101:3516:1883 2:N:0 145 chr1 29695606 255 94M * 0 0
GGTGGCCCTGGTGG
HWI-ST1269:287:H9BA4ADXX:1:1101:3516:1883 1:N:0 321 chr1 29694857 255 29M * 0 0
CGAGCTGGAGACTG
HWI-ST1269:287:H9BA4ADXX:1:1101:3516:1883 1:N:0 321 chr1 29695224 255 69M * 0 0
GGGTTGTGGAAACC
HWI-ST1269:287:H9BA4ADXX:1:1101:3778:1975 1:N:0 83 chr1 29678425 255 99M =
29674081 -4250
The header of the output bam file has been changed successfully, but the column
related to chrmosome_id has been converted into chr1, it's not the fruit I want.
Samtools-Version: 0.1.19-44428cd
I don't know why it comes and how to solve it.
Best regards,
Jessie
Jessie Yang
Bioinformatic Research
Annoroad Gene Technology, China
Building B2, Yizhuang Biomedical Park, Kechuang 6 Rd,
Beijing Economic-Technologic al Development Area ,Beijing, China, 100176
Email:jiey...@annoroad.com
Tel: +86 15311439112
Website: www.annoroad.com
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