Hi Josh,
here is the header information I get:
samtools view -H ./output/KMT/9557-FGS-R.sam
@SQ SN:B.FR.1983HXB2-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 bysamtools
view -H sample_file.sam
Josh Bradley
On Thu, Jul 2, 2015 at 8:01 AM, <[email protected]>
wrote:
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Date: Thu, 02 Jul 2015 12:48:06 +0200
From: [email protected]
Subject: [Samtools-help] Header
To: [email protected]
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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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