Hello! I am working on a script for a VCF pipeline.
I currently receive the following error in my bwa step....
line 22: 3354610 Killed bwa mem bwaParts my_lovely_file_trimmed.fq > $bwa_sam
...This is a memory issue that I need to speak to my supervisor about, nonetheless because of this, the SAMtools and GATK commands downstream don't work.
Even though I am dealing with this error early in the pipeline I still want to know if the samtools and GATK syntax is correct, and will work once the memory issue is resolved.
Here is the code
samtools sort $bwa_sam -o $sam_sam gatk AddOrReplaceReadGroups -I sorted_sam -O GATK_bam -RGLB lib1 --RGPL illumina --RGPU unit1 --RGSM file
If you're well seasoned- like a steak at Gordan Ramsey's restaurants- at these commands, please take a peak for my sanity.
All the best, Gilgy
P.S bwaParts are the amb,ann,bwt,pac,sa files from the bwa index command.