Labelling

GW is designed to make manually labelling 100s - 1000s of variants as pain free as possible. Using the command-line interface, labels can be saved to a tab-separated file and opened at a later date to support labelling over multiple sessions. GW can also write a modified VCF, updating the filter column with curated labels.

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Use the UP and DOWN arrows to increase or decrease the number of image tiles, or LEFT and RIGHT to navigate through images. Below is a view of 196 variant images.

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To use labelling correctly in GW, ensure all variant IDs in your input VCF/BCF are unique - this should normally be the case anyway.

When you open a VCF file, GW will parse the ‘filter’ column and display this as a label in the bottom left-hand corner of image tiles. Other labels can be parsed from the VCF using the –parse-label option. For example, the SU tag can be parsed from the info column using:

gw hg38.fa -b your.bam -v variants.vcf --parse-label info.SU

Image tiles can then be clicked-on using the mouse to modify the label, choosing between PASS/FAIL by default. To provide a list of alternate labels, use the --labels option:

gw hg38.fa -b your.bam -v variants.vcf --labels Yes,No,Maybe

Now, when you left-click on a tiled image, you can cycle through this list.

To save or open a list of annotations, use the --in-labels and --out-labels options. This makes it straightforward to keep track of labelling progress between sessions. Only variants that have been displayed to screen will be appended to the results in --out-labels file. The same file can be used for in and out labels, if desired:

gw hg38 -b your.bam -v variants.vcf --in-labels labels.tsv --out-labels labels.tsv

Labels are output as a tab-separated file with the following format:

chrom pos variant_ID label var_type labelled_date variant_filename
chr1 200000 27390 PASS DEL   test.vcf
chr1 250000 2720 FAIL SNP 14-10-2022 16-05-46 test.vcf

The labelled_date column is only filled out if one of the tiled images was manually clicked - if this field is blank then the --parsed-label was used. This feature allows you to keep track of which variants were user-labelled over multiple sessions. Additionally, the --out-labels file is auto-saved every minute for safe keeping.

GW can also write labels to a VCF file. We recommend using this feature to finalise your annotation - the whole VCF file will be written to --out-vcf. The final label will appear in the ‘filter’ column in the vcf. Additionally, the date and previous filter label are kept in the info column under GW_DATE, GW_PREV:

gw hg38.fa -b your.bam -v variants.vcf --in-labels labels.tsv --out-vcf final_annotations.vcf

Note, the --in-labels option is not required here, but could be used if labelling over multiple sessions, for example. Also, a GW window will still pop-up here, but this could be supressed using the --no-show option.