Alignments and variants

Loading alignment data

Drag-and-drop a BAM/CRAM into the window, use the load command (tab-completion works), or the --bam/-b option:

gw hg38 -b your.bam -r chr1:1-20000

The hg38 argument is a genome-tag from the config file. For much faster performance, point the tag at a local FASTA — see Settings.

Multiple -b options stack BAMs vertically; multiple -r options split the window into regions.

If a genome-tag matches the BAM header SQ lines, the file can be opened directly:

gw your.bam

GW reads the BAM header and infers the reference genome. This also makes the macOS/Linux Open with association work.

Screenshot placeholder — alignment view with coverage, mismatches, indels
docs/assets/images/v2/alignments.png

Working with reads

  • Click a read to select it and open the read popup (SAM fields, tags, mate add, find)
  • Toggle display elements with the view dropdown or toggle commands: insertions, mismatches, base modifications, edges, soft-clips
  • sort reads by strand, haplotype or base at a position
  • filter reads (e.g. filter mapq >= 10)

Base modifications

Display base modifications (MM/ML tags) with the --mods option or the mods command.

Splice junctions

--introns or the introns command draws a splice-junction track per BAM. Junctions are clustered (--splice-cluster-eps) and filtered by supporting reads (--min-junction-reads).

Structural variants

link sv draws linking lines between the split alignments of a structural variant; link none clears them. v / var shows the variant under the cursor.

Variant files

A variant file (VCF/BCF/BED) can be opened by drag-and-drop or with -v. Depending on vcf_as_tracks, variants are drawn as a track or as image tiles.

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