Have you tried running your samtools conversion command on another sample
file first to make sure the problem isn't samtools? Also what version of
samtools do you have? Try this
<https://code.google.com/p/bamseek/downloads/detail?name=ex1.sam> small
file and run
samtools view -b ex1.sam > ex1.bam
Assuming it works correctly, you should be able to do
samtools view -h ex1.bam | more
and see the original file contents again.
If you're using the latest version of samtools, you don't need the -S flag.
I believe that's been left in for backwards compatibility reasons. Samtools
will automatically detect SAM/BAM format of an input file. As a point of
reference, the ex1.sam file is 559523 bytes in size. Afterwards, ex1.bam
should be 126661 bytes.
Josh Bradley
On Mon, Jul 6, 2015 at 7:04 AM, <[email protected]> wrote:
> Hi Josh,
>
>
>
> here is the header information I get:
>
>
>
> samtools view -H ./output/KMT/9557-FGS-R.sam
> @SQ SN:B.FR.1983.HXB2-LAI-IIIB-BRU.K03455 LN:9719
> @PG ID:bwa PN:bwa VN:0.7.12-r1044 CL:bwa mem -aCHMpP
> ./ref/HXB2.fasta ./KMT/9557-FGS-R-R1.fastq.gz ./KMT/9557-FGS-R-R2.fastq.gz
>
>
>
> I read something about the -C parameter and retried with
>
> bwa mem -aHMpP instead of bwa mem -aCHMpP, but the header looks the same:
>
>
>
> samtools view -H ./output/KMT/9557-FGS-R.sam
> @SQ SN:B.FR.1983.HXB2-LAI-IIIB-BRU.K03455 LN:9719
> @PG ID:bwa PN:bwa VN:0.7.12-r1044 CL:bwa mem -aHMpP
> ./ref/HXB2.fasta ./KMT/9557-FGS-R-R1.fastq.gz ./KMT/9557-FGS-R-R2.fastq.gz
>
> At least I am then able to create the bam file for whatever reason. Do you
> know why? Thanks for helping,
>
> Marcel
>
>
> -----Ursprüngliche Nachricht-----
> Von: "Joshua Bradley" [[email protected]]
> Gesendet: Do. 02.07.2015 16:28
> An: [email protected]
> Betreff: Re: [Samtools-help] Header
>
> Can you post the header information from the files? You can get it by
> samtools view -H sample_file.sam
>
> Josh Bradley
>
> On Thu, Jul 2, 2015 at 8:01 AM, <
> [email protected] <#14e630d489b174c4_>> wrote:
>
>> Send Samtools-help mailing list submissions to
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>> 1. Header ([email protected] <#14e630d489b174c4_>)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 02 Jul 2015 12:48:06 +0200
>> From: [email protected] <#14e630d489b174c4_>
>> Subject: [Samtools-help] Header
>> To: [email protected] <#14e630d489b174c4_>
>> Message-ID: <[email protected]
>> <#14e630d489b174c4_>>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear all,
>> ?
>> I used
>>
>>
>> ?? bwa mem -aCHMpP ...
>> ?
>> in order to create .sam files for my pair-end reads data.
>> When I try to perform the command
>>
>>
>> ?? samtools? view -bS ...
>>
>>
>> in order to convert the .sam to .bam files, I get the following error
>> message:
>> ?
>> ?? [E::sam_parse1] unrecognized type
>> ?? [W::sam_read1] parse error at line 3
>> ?? [main_samview] truncated file.
>> ?
>> During my web search I could only find information about custom read
>> annotations leading to this error which I don't provide.
>> Could anybody tell me what I am missing?
>> ?
>> Kind regards,
>> Marcel
>>
>>
>> ---
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