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blog/sort_by_barcode.md

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+---
+author: Pavel Dimens
+date: 2024-11-05
+category: guides
+description: Sorting data by linked-read barcode
+icon: sync
+image: https://visualpharm.com/assets/214/Merge%20Files-595b40b75ba036ed117d8636.svg
+---
+
+# :icon-sync: Sort data by barcode
+You would think sorting data would be a no-brainer, and in most cases it is.
+You can use `seqtk` or `seqkit` to sort FASTQ/A files by their IDs, `samtools` to sort
+SAM/BAM/CRAM files by name or coordinates. However, in the world of linked-read
+data, sometimes you may need to sort your FASTQ (or BAM) files by the
+linked-read barcode. The way to do that wasn't initially obvious to the Harpy/haplotag
+team, so this article serves to make this knowledge widely available to linked-read
+adopters.
+
+## Sorting Alignments
+Let's start with BAM (or SAM/CRAM) files because the process is much simpler.
+Since the linked-read barcode is stored in a `BX:Z` tag (or less often as `BC:Z:`),
+we can use a little feature of `samtools sort` to guide the sort by the barcode:
+> -n TAG     Sort first by the value in the alignment tag TAG, then by position or name (if also using -n or -N). 
+```bash
+
+```