On 6 Jul 2015, at 12:04, [email protected] wrote:
> 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.
The bwa documentation for mem -C says
Note that the FASTA/Q comment (the string after a space in the header
line)
must conform [to] the SAM spec (e.g. BC:Z:CGTAC). Malformated comments
lead to incorrect SAM output.
If you look at line 3 of your broken BAM file (the first non-header record
line) I think you will see that the comment that's come from your FASTA
reference file is just plain text rather than something that looks like SAM
tagged fields (like BC:Z:...).
John
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