BWA (Burrows-Wheeler Aligner)

Overview

BWA (Burrows-Wheeler Aligner) is a short-read alignment tool for mapping sequencing reads to a reference genome using the Burrows-Wheeler transform. It includes three algorithms: BWA-backtrack (for reads ≤100 bp), BWA-SW (for longer reads with local alignment), and BWA-MEM (the current standard, suitable for 70 bp – 1 Mb reads). BWA-MEM is the most widely used for WGS and WES alignment in cancer genomics pipelines and is distributed with the Broad GATK best-practices workflow.

Used by

  • Used to align paired tumor/normal WGS reads to hg19 for 28 metastatic neuroendocrine neoplasms in the BC Cancer POG program; downstream SNV/indel calling performed by Strelka, SV calling by ABySS/Trans-ABySS PMID:24326773.
  • Used for read alignment in paired tumor/normal whole-exome sequencing of grade II glioma initial/recurrent pairs (n=23) PMID:24336570
  • BWA used to align paired-end 100-bp reads from low-pass whole-genome sequencing (1-3x) of four FFPE prostate needle biopsies to hg19 as a proof-of-principle for CNA burden measurement in diagnostic biopsies PMID:25024180
  • Used for sequence alignment in the MSK-IMPACT pipeline for 69 matched CRC primary/metastasis trios. PMID:25164765
  • Used for read alignment to GRCh37-lite in Ewing sarcoma WGS study (112 tumors with matched germline) PMID:25223734
  • Used for WES read alignment to GRCh37/hg19 in nccRCC study (167 primary tumors, 140 tumor-normal pairs) PMID:25401301
  • Used for read alignment in WES pipeline processing 29 AA CRC tumor/normal discovery exomes in the MSS African American CRC landscape study PMID:25583493
  • BWA used to align reads to UCSC hg19 in 109 microdissected PDA WES samples prior to MuTect/VarScan variant calling. PMID:25855536
  • BWA used together with Picard and Firehose at the Broad Institute to align reads from 320 melanoma WES and WGS samples to the reference genome. PMID:26091043
  • BWA used for read alignment in whole-exome sequencing of adrenocortical carcinoma PMID:26095796
  • BWA used for read alignment in targeted panel sequencing (MSK-IMPACT) of pancreatic cancer PMID:26278805
  • BWA used for read alignment in whole-exome and whole-genome sequencing of colorectal cancer PMID:26343386
  • Used to align paired-end whole-exome sequencing reads (BWA v0.5.9) to hg19 in a 42-patient CTCL study defining the mutational landscape of Sézary syndrome and mycosis fungoides PMID:26551667.
  • Used for alignment in whole-genome sequencing of 28 uveal melanoma samples with GRCh37 reference, followed by GATK indel realignment and base quality recalibration; enabled discovery of the recurrent PLCB4 p.D630Y hotspot PMID:26683228.
  • Used for alignment of whole-genome sequencing reads to GRCh37-lite in 46 matched diagnostic/recurrence medulloblastoma samples; enabled characterization of massive genetic divergence between primary and recurrent tumours PMID:26760213.
  • BWA used for read alignment in the HGSC Mercury pipeline processing whole-exome sequencing data from 160 periampullary tumors on HiSeq 2000; followed by GATK recalibration and Atlas/PInDel variant calling PMID:26804919
  • bwa v0.7.1 used for alignment of WES reads from 141 tumors of 56 men with metastatic CRPC (prad_fhcrc), followed by GATK indel realignment and MuTect somatic mutation calling. PMID:26928463
  • BWA-MEM used for read realignment in 619 CRC FFPE tumor/normal WES pairs prior to SNV/indel calling with MuTect and Indelocator/Strelka PMID:27149842
  • Used for read alignment in the NSCLC pan-lung WES study covering 1,144 tumor/normal pairs (660 ADC + 484 SqCC) PMID:27158780
  • BWA-MEM used to align tumour and matched-normal reads to hg19 for MSK-IMPACT sequencing in 62 uRCC tumours; average coverage 348x tumour / 280x normal. PMID:27713405
  • BWA-MEM used for read alignment of 216 metastatic breast cancer whole-exome sequencing samples before GATK base recalibration and MuTect/Scalpel mutation calling PMID:28027327.
  • Used for read alignment in the TCGA esophageal/stomach multi-platform study across 164 oesophageal carcinomas and 359 gastric adenocarcinomas PMID:28052061.
  • Used BWA for short-read alignment to the reference genome in WGS/WES pipelines PMID:28373299
  • BWA MEM used for alignment to hg19 in the MSK-IMPACT bioinformatics pipeline, followed by ABRA realignment and GATK base-quality recalibration PMID:28481359
  • Used for alignment of whole-genome sequencing reads (Illumina HiSeq X10/2500/2000) in the ICGC cholangiocarcinoma study (n=71 WGS tumor/normal pairs) PMID:28667006
  • BWA mem alignment to hg19 applied in the DLBCL whole-exome sequencing pipeline for 1001 tumors PMID:28985567
  • BWA v0.7.15 used to align WES reads to hg19 for 15 Korean vulvar SCC tumor/normal pairs; followed by Picard v2.7.1 and Samtools v1.3.1 de-duplication and GATK v3.6 local realignment/BQSR PMID:29422544

Notes

  • BWA-MEM is the recommended algorithm for reads ≥70 bp; BWA-backtrack was standard for early Illumina CASAVA-era data.
  • PCR duplicate marking (e.g., Picard MarkDuplicates, samblaster) is typically applied after BWA alignment.
  • Output is SAM/BAM format; coordinate-sorted and indexed BAMs are required for most downstream tools.

Sources

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