Finding BAM dataset identifiers

Authors: orcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-JacksonMelkeberhan Berhanu Degefa avatar Melkeberhan Berhanu DegefaAdd Contributions!
How to find the reference sequence identifiers inside of a BAM file

Explore the content of your BAM.

  1. Run Samtools: IdxStats on your bam dataset.
  2. The reference sequence identifiers inside the “BAM header” will be listed in the result report.
  3. The report is a summary of the BAM content that includes: reference sequence identifiers (chromosome names), their lengths, and a count of the reads mapping to that reference sequence within the BAM file.
  4. Compare the sequence identifiers in your BAM file to the the sequence identifiers (aka “chrom” field) field in all other inputs: VCF, GTF, GFF3, BED, Interval, Tabular.
  5. It is usually important to use the same reference assembly for all steps within the same analysis. If you discover differences, you may need to choose different reference data.

Notes

  • This method will not work for “sequence-only” bam datasets, as these usually have no header and are not associated with a reference assembly yet.
Persistent URL
Resource PURL: https://gxy.io/GTN:F00023
Still have questions?
Gitter Chat Support
Galaxy Help Forum