Remapping an aligned BAM

This is a short post on how to remap short reads in an aligned BAM using bwa-mem. My recommendation is (requiring bash)

samtools collate -Oun128 in.bam | samtools fastq -OT RG,BC - \
  | bwa mem -pt8 -CH <(samtools view -H in.bam|grep ^@RG) ref.fa - \
  | samtools sort -@4 -m4g -o out.bam -

Here, samtools collate groups the two reads in a read pair and outputs an uncompressed BAM stream. samtools fastq consumes this stream and generates an interleaved FASTQ. Option -T RG,BC copies RG and BC tags in the input BAM to the output FASTQ comment lines. bwa mem -C then copies these tags to the output SAM. Option -H <(...) inserts header @RG lines. Option -p processes an interleaved FASTQ stream. Finally, samtools sort generates sorted BAM. I often use -@4 -m4g for faster sorting. If you have unaligned BAM (aka uBAM), you can skip the first collate step.

I wrote about design command-line interface a couple of days ago. This posts exemplifies the power of a proper design: you can chain multiple tools together to achieve high performance without writing any high-performance code.