/software-guides

How to fix truncated BAM files from BWA?

Learn to fix truncated BAM files from BWA with diagnostic checks, repair methods, re-creation tips, and preventive measures for data integrity and future protection.

Get free access to thousands LifeScience jobs and projects!

Get free access to thousands of LifeScience jobs and projects actively seeking skilled professionals like you.

Get Access to Jobs

How to fix truncated BAM files from BWA?

 

Understand the Issue

 

  • Truncated BAM files often result from incomplete file transfers or interruptions during the BWA alignment process.
  •  

  • BAM files are binary, so corruption isn't always visually apparent. They may fail during downstream processing or when converting to SAM format.

 

Diagnostic Check

 

  • Use `samtools quickcheck` to identify issues with the BAM file without reading all contents. It checks for termination issues.
  •  

  • Check the file header using `samtools view -H yourfile.bam`. Ensure the header loads correctly.

 

Repair the BAM File

 

  • Use `samtools` to attempt repairs. The command `samtools quickcheck -r yourfile.bam` can sometimes recover partially written BAM files.
  •  

  • Convert BAM to SAM using `samtools view yourfile.bam > yourfile.sam`. This process sometimes circumvents issues in reading the BAM file.

 

Re-create the BAM File

 

  • If repairs fail, regenerate the BAM file from raw data. Rerun the BWA alignment process from original FASTQ files, if available.
  •  

  • Ensure sufficient storage space and stable system resources during re-creation to prevent future truncations.

 

Preventive Measures

 

  • Maintain a robust data backup and integrity check routine. Use checksum verification to ensure file integrity before and after file transfers.
  •  

  • Regularly update `samtools` and BWA to the latest versions to benefit from improvements in handling such issues.

Explore More Valuable LifeScience Software Tutorials

How to optimize Bowtie for large genomes?

Optimize Bowtie for large genomes by tuning parameters, managing memory, building indexes efficiently, and using multi-threading for improved performance and accuracy.

Read More

How to normalize RNA-seq data in DESeq2?

Guide to normalizing RNA-seq data in DESeq2: Install DESeq2, prepare data, create DESeqDataSet, normalize, check outliers, and use for analysis.

Read More

How to add custom tracks in UCSC Browser?

Learn to add custom tracks to the UCSC Genome Browser. This guide covers data preparation, uploading, and customization for enhanced genomic analysis.

Read More

How to interpret Kraken classification outputs?

Learn to interpret Kraken outputs for taxonomic classification, from setup and input preparation to executing commands, analyzing results, and troubleshooting issues.

Read More

How to fix STAR index generation issues?

Learn to troubleshoot STAR index generation by checking software compatibility, verifying input files, adjusting memory settings, and consulting documentation for solutions.

Read More

How to boost HISAT2 on HPC systems?

Boost HISAT2 on HPC by optimizing file I/O, tuning parameters, leveraging scheduler features, utilizing shared memory, monitoring performance, executing in parallel, and fine-tuning indexing.

Read More

Join as an expert
Project Team
member

Join Now

Join as C-Level,
Advisory board
member

Join Now

Search industry
job opportunities

Search Jobs

How It Works

1

Create your profile

Sign up and showcase your skills, industry, and therapeutic expertise to stand out.

2

Search Projects

Use filters to find projects that match your interests and expertise.

3

Apply or Get Invited

Submit applications or receive direct invites from companies looking for experts like you.

4

Get Tailored Matches

Our platform suggests projects aligned with your skills for easier connections.