[Bioc-sig-seq] different results between Rsamtools and samtools

[Ivan Gregoretti]

Just for the purpose of documenting, this is your shortcut to get the
problem solved:

http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader

Ivan




On Tue, Sep 28, 2010 at 10:15 AM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> Hi Ivan,
>
> thanks a lot...
>
> This happens to 2 files I have (that's why I think the problem is with
> the files)... So, the header (using samtools view -H) is concordant
> with Rsamtools...
>
> @SQ     SN:chr10        LN:135374737
> @SQ     SN:chr11        LN:0
> @SQ     SN:chr12        LN:0
> @SQ     SN:chr13        LN:0
> @SQ     SN:chr14        LN:0
> @SQ     SN:chr15        LN:0
> @SQ     SN:chr16        LN:0
> @SQ     SN:chr17        LN:0
> @SQ     SN:chr18        LN:0
> @SQ     SN:chr19        LN:0
> @SQ     SN:chr1 LN:0
> @SQ     SN:chr20        LN:0
> @SQ     SN:chr21        LN:46944323
> @SQ     SN:chr22        LN:0
> @SQ     SN:chr2 LN:0
> @SQ     SN:chr3 LN:0
> @SQ     SN:chr4 LN:0
> @SQ     SN:chr5 LN:0
> @SQ     SN:chr6 LN:0
> @SQ     SN:chr7 LN:0
> @SQ     SN:chr8 LN:0
> @SQ     SN:chr9 LN:0
> @SQ     SN:chrM LN:0
> @SQ     SN:chrX LN:0
> @SQ     SN:chrY LN:57772954
>
> So, the header seems to be the culprit...
>
> Thank you very much,
>
> b
>
>
> On 28 September 2010 15:06, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>> Hi Benilton,
>>
>> Does this happen with all your BAM files?
>>
>> Check the header in the BAM file. For mouse, it should look like this:
>>
>> samtools view -H myfile.bam
>> @HD     VN:1.0  SO:coordinate
>> @SQ     SN:chr1 LN:197195432
>> @SQ     SN:chr2 LN:181748087
>> @SQ     SN:chr3 LN:159599783
>> @SQ     SN:chr4 LN:155630120
>> @SQ     SN:chr5 LN:152537259
>> @SQ     SN:chr6 LN:149517037
>> @SQ     SN:chr7 LN:152524553
>> @SQ     SN:chr8 LN:131738871
>> @SQ     SN:chr9 LN:124076172
>> @SQ     SN:chr10        LN:129993255
>> @SQ     SN:chr11        LN:121843856
>> @SQ     SN:chr12        LN:121257530
>> @SQ     SN:chr13        LN:120284312
>> @SQ     SN:chr14        LN:125194864
>> @SQ     SN:chr15        LN:103494974
>> @SQ     SN:chr16        LN:98319150
>> @SQ     SN:chr17        LN:95272651
>> @SQ     SN:chr18        LN:90772031
>> @SQ     SN:chr19        LN:61342430
>> @SQ     SN:chrX LN:166650296
>> @SQ     SN:chrY LN:15902555
>> @SQ     SN:chrM LN:16299
>> @SQ     SN:chr13_random LN:400311
>> @SQ     SN:chr16_random LN:3994
>> @SQ     SN:chr17_random LN:628739
>> @SQ     SN:chr1_random  LN:1231697
>> @SQ     SN:chr3_random  LN:41899
>> @SQ     SN:chr4_random  LN:160594
>> @SQ     SN:chr5_random  LN:357350
>> @SQ     SN:chr7_random  LN:362490
>> @SQ     SN:chr8_random  LN:849593
>> @SQ     SN:chr9_random  LN:449403
>> @SQ     SN:chrUn_random LN:5900358
>> @SQ     SN:chrX_random  LN:1785075
>> @SQ     SN:chrY_random  LN:58682461
>>
>> I suspect that you have a corrupt header.
>>
>> Ivan
>>
>>
>>
>>
>>
>> On Tue, Sep 28, 2010 at 9:28 AM, Benilton Carvalho
>> <beniltoncarvalho at gmail.com> wrote:
>>> Hi,
>>>
>>> I wonder if you guys could help me out understanding what the problem
>>> may be when reading in some BAM files I have...
>>>
>>> When viewing them with samtools, I get reads on chr6 (samtools view
>>> file.bam chr6)
>>>
>>> When using scanBam/scanBamHeader, I do not get any reads on chr6
>>> (latest RSamtools on 2.11.1, but same happens with the latest devel
>>> too).
>>>
>>> Suggestions on how to proceed in order to understand what may be going
>>> on (or what I may be missing)? My guess is that the files are
>>> corrupted, nothing strange comes up when using samtools...
>>>
>>> Thank you,
>>>
>>> benilton
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>
>>
>