What do you recommend I use to insert full command line into the BAM header created with BWA. BWA already creates this:
@PG ID:bwa PN:bwa VN:0.5.9-r16
But I'd like to capture the whole process (aln and sampe) and insert them as CL tags.
Tophat does it nicely like this for example:
@PG ID:TopHat VN:1.2.0 CL:/packages/tophat-1.2.0/tophat -r 43 -p 8 -o /some/path/s_1_topHat -G /some/path/Homo_sapiens.NCBI36.54.noMT.gtf /some/path/human_b36_both_noM /some/path/s_1_1.fastq /some/path/s_1_3.fastq
@PG ID:bwa PN:bwa VN:0.5.9-r16
But I'd like to capture the whole process (aln and sampe) and insert them as CL tags.
Tophat does it nicely like this for example:
@PG ID:TopHat VN:1.2.0 CL:/packages/tophat-1.2.0/tophat -r 43 -p 8 -o /some/path/s_1_topHat -G /some/path/Homo_sapiens.NCBI36.54.noMT.gtf /some/path/human_b36_both_noM /some/path/s_1_1.fastq /some/path/s_1_3.fastq
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