bwa aln pipeline
- bwa mapping + dedup
- bwa hybrid mapping + dedup + split
The pipeline works for single references such as GRCh37 and GRCh38, as well as hybrid genomes (e.g. mm9+dm3).
dependencies
- bwa
- python 2.7
- SJM (simple job manager)
- bgzip and tabix 1.2.1
- LSF batch system (or other)
set up module
export MODULEPATH=$MODULEPATH:/dir/to/bwamapping/modulefiles module load bwamapping
run module
run_bwa_aln.py -r1 ../fq/_R1.fastq -r2 ../fq/_R2.fastq -o b37.bam -O pwd --id NA12878 --pl ILN --sm NA12878 --lb GIAB --tmp /scratch_space -j b37.sjm
understand ID and SM in RG tag
ID:
- ID is taged for each read in teh BAM
- ID do not need to carry any meaning as it is used as uniq key.
- Can be used to distinguish the reads from different experiments. for example if your initial sequencing does not have enough coverage, and a topoff was done to get more reads. ID could be "NA12878" and "NA12878-topoff" to distinguish every reads.
SM:
- Every BAM is encouraged to have one SM tag, unless in rare scenario you need to merge numtiple samples together.
- SM is used by GATK as sample name in variant call step (write to VCF file). if there are multiple SM tag in a BAM GATK HC caller (gvcf mode) would be confused.
- SM can be identical to ID for one sample, one experiemnts cases.