On Thu, 14 Mar 2019, Aengus Stewart wrote:
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
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
-
Your fastq comments need to be valid SAM tags. From the BWA manual page:
-C Append FASTA/Q comment to SAM output. This option can
be used to transfer read meta information (e.g. bar‐
code) to the SAM output. Note that the FASTA/Q comment
(the string after a space in the header line) must
conform the SAM spec (e.g. BC:Z:CGTAC). Malformated
comments lead to incorrect SAM output.
So if you want to put a barcode sequence into the SAM BC tag, you would
need something like this:
@M02212:177:000000000-CBJHK:1:1101:11456:1264 BC:Z:AGGCAGAA-CTCTCTAT
Rob Davies r...@sanger.ac.uk
The Sanger Institute http://www.sanger.ac.uk/
Hinxton, Cambs., Tel. +44 (1223) 834244
CB10 1SA, U.K. Fax. +44 (1223) 494919
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