Labelling
GW makes manually labelling hundreds–thousands of variants as pain-free as possible. Labels save to a tab-separated file and can be re-opened later, supporting labelling over multiple sessions. GW can also write a modified VCF with labels in the filter column.
docs/assets/images/v2/label_table.png Basic workflow
- Open a VCF with
-vso variants are drawn as image tiles ↑/↓changes the number of tiles;←/→navigates- Left-click a tile to cycle labels
- Save with
save labels/--out-labels; reload with--in-labels
gw hg38 -b your.bam -v variants.vcf --in-labels labels.tsv --out-labels labels.tsv
Ensure all variant IDs in the input VCF/BCF are unique.
Labels and comments
By default GW parses the VCF filter column as the label. Parse another field with --parse-label:
gw hg38 -b your.bam -v variants.vcf --parse-label info.SU
Custom label list:
gw hg38 -b your.bam -v variants.vcf --labels Yes,No,Maybe
To add a comment, move the mouse over the tile, open the command box and type " or ' followed by the comment. The comment attaches to the label (orange dot) and is saved in the output.
Label file format
Tab-separated columns:
| chrom | pos | variant_ID | label | var_type | labelled_date | variant_filename | comment |
|---|---|---|---|---|---|---|---|
| chr1 | 200000 | 27390 | PASS | DEL | test.vcf | ||
| chr1 | 250000 | 2720 | FAIL | SNP | 14-10-2022 16-05-46 | test.vcf |
labelled_date is only filled when a tile was manually clicked — blank means the label came from --parse-label. --out-labels auto-saves every minute.
Writing labels to a VCF
Writes the whole VCF to --out-vcf, with the final label in the filter column. Date and previous filter are kept under GW_DATE and GW_PREV:
gw -v input_variants.vcf --in-labels labels.tsv --out-vcf output_variants.vcf