Entering edit mode
9.2 years ago
anailg92
•
0
Hi, I'm doing a GWAs study in Arabidopsis thaliana, I'm using for preprocessing the samples the commands bwa aln
and sampe
, then samtools import reference.fa sample.sam sample.bam
.
But when the script continous, it has an error and I don't know how to fix. This is my error:
[samopen] SAM header is present: 7 sequences.
[sam_read1] reference 'ID:bwa PN:bwa VN:0.7.10-r789 CL:/home/bwa-0.7.10/
bwa sampe ./thaliana.fa SRR519713_1.sai SRR519713_2.sai SRR519713_1.fastq SRR519713_2.fastq
' is recognized as '*'.
[main_samview] truncated file.
If anyone knows where I am wrong?
And another question which reference genome I have to put in this command line:
java -Xmx4g -jar $HOME/opt/GATK2/GenomeAnalysisTK.jar -T RealignerTargetCreator -R $2 -I $3.bam -o $3
Thank you!
What command are you giving that produces that error message? It looks like the header is completely messed up. BTW, use
samtools view
instead ofsamtools import
.