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

[Benilton Carvalho]

very useful... thank you. b

On 28 September 2010 15:22, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> 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
>>>>
>>>> _______________________________________________
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>>>> Bioc-sig-sequencing at r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>>>
>>>
>>
>