plot for MBQ

juanjo255 · Oct 31, 2024 · f2c55bb · f2c55bb
1 parent 18b1a03
commit f2c55bb
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Showing 3 changed files with 12 additions and 1 deletion.
diff --git a/example_vcf_plots/median-base-quality-by-allele.boxplot.png b/example_vcf_plots/median-base-quality-by-allele.boxplot.png
diff --git a/scripts/custom_macro.py b/scripts/custom_macro.py
@@ -11,3 +11,8 @@ def POS(variant):
 def AF(variant):
     """Get allele fractions of alternate alleles as a numpy array."""
     return np.concatenate([variant.format("AF").flatten()])
+
+@continuous
+def MBQ(variant):
+    """Get median base quality by allele as a numpy array."""
+    return [i for i in variant.INFO["MBQ"]]
diff --git a/scripts/plots_vcf.toml b/scripts/plots_vcf.toml
@@ -51,4 +51,10 @@ figtype = 'bar'
 formula = 'DEPTHs ~ 1'
 title = 'Number of positions per depth'
 ggs = 'stat_bin(bins=5);theme_light(); ylab("# Positions");xlab("Read-depth")'
-figtype = 'histogram'
+figtype = 'histogram'
+
+[[instance]]
+formula = 'MBQ ~ CHROM'
+title = 'Median base quality by allele'
+ggs = 'theme_light(); ylab("MBQ");xlab("CHROM")'
+figtype = 'boxplot'