• 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).

• bwa
• python 2.7
• SJM (simple job manager)
• bgzip and tabix 1.2.1
• LSF batch system (or other)

export MODULEPATH=$MODULEPATH:/dir/to/bwamapping/modulefiles module load bwamapping

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

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.

https://github.com/StanfordBioinformatics/SJM