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update VirHEAT to v0.7, add -a and -s (galaxyproject#6026)
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* update to v0.7, add -a and -s

* use column_names instead of text

* Update virheat.xml

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Co-authored-by: Björn Grüning <[email protected]>
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PlushZ and bgruening authored May 28, 2024
1 parent 01204be commit 5ae40d4
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Showing 4 changed files with 16,173 additions and 4 deletions.
6 changes: 4 additions & 2 deletions tools/virheat/macros.xml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">0.6</token>
<token name="@TOOL_VERSION@">0.7</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">21.01</token>
<xml name="biotools">
Expand All @@ -22,12 +22,14 @@ What it does
============
This tool generates multi-sample variant-frequency plots from SnpEff-annotated
viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.
viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time.
The tool expects either the length of a reference genome or the gff3 file if the sequence annotation is needed.
Additionally, to analyze whether mutations are sufficiently covered and to display non-covered cells in grey, first create per-base coverage TSV files for each BAM file with Qualimap and provide them in the same folder as the VCF files. Give them the same name as your VCF files.
Moreover, there is an option to include visualizations of additional scores (e.g., MAVE scores for binding affinity, expression level, antibody escape, etc.) mapped to mutations on the heatmap.
The tool expects input variant lists in VCF format. VCF datasets as produced by standard variant callers with
- variant allele frequencies encoded in an ``AF`` INFO field
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