The relevant man pages are pretty clear on this question:
bio-bwa.sourceforge.net/bwa.shtml
samtools.github.io/hts-specs/SAMv1.pdf
The comment string following the space in each fastq header line
needs to conform to the SAM spec for user-defined optional fields,
and the example shown does not. One probably needs to write a sed
script that alters the header lines into an acceptable format.
- tom blackwell -
On Thu, 14 Mar 2019, Aengus Stewart wrote:
Hi guys,
Our sequencer is now outputting header lines with the following format
@M02212:177:000000000-CBJHK:1:1101:11456:1264 1:N:0:AGGCAGAA+CTCTCTAT
If I use BWA with the -C flag then this header info gets sent to the .sam output
file however in the sam->bam conversion I am
getting
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 202164 reads in 14.429 CPU sec, 3.606 real sec
[E::sam_parse1] unrecognized type :
[W::sam_read1] Parse error at line 11
samtools sort: truncated file. Aborting
User: 14.22
System: 0.62
Elapsed: 0:04.21
I am running modules for SAMtools/1.9-foss-2018b BWA/0.7.17-foss-2018b
my default commandline would look like
bwa mem -t 4 -M -B 2 -C -R
"@RG\tID:B-Zhejiang-Wuxin-113-2018_QFX\tLB:B-Zhejiang-Wuxin-113-2018_QFX\tSM:B-Zhejiang-Wuxin-113-2018_QFX\tPL:ILLUMINA"
\
/camp/stp/babs/working/stewara/projects/asf/laura.cubitt/RN19003/reference/swH1N1
\
B-Zhejiang-Wuxin-113-2018_QFX.R1.trim.fastq \
B-Zhejiang-Wuxin-113-2018_QFX.R2.trim.fastq | \
samtools sort -@4 -O BAM -o B-Zhejiang-Wuxin-113-2018_QFX.swH1N1.test.bam
-
Cheers
Aengus
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Head of Bioinformatics and BioStatistics
Francis Crick Institute
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