Issue #228 | now mask bad genotype sites as het

README.md

@@ -297,7 +297,7 @@ Character | Meaning
 `-`       | Zero coverage in this sample **or** a deletion relative to the reference
 `N`       | Low coverage in this sample (based on `--mincov`)
 `X`       | Masked region of reference (from `--mask`)
-`n`       | Heterozygous site in this sample (has `GT=0/1` in `snps.raw.vcf`)
+`n`       | Heterozygous or poor quality genotype  (has `GT=0/1` or `QUAL<--minqual` in `snps.raw.vcf`)
 
 You can remove all the "weird" characters and replace them with `N` using the included
 `snippy-clean_full_aln`.  This is useful when you need to pass it to a tree-building

bin/snippy

@@ -463,13 +463,14 @@ while (<$depth_fh>) {
 close $depth_fh;
 
 # . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
-# go back and patch in 'n' at all heterozygous sites
+# go back and patch in 'n' at all heterozygous sites and low QUAL sites
 # these could be 0/1, or 1/2 even, so we select any "het" site
 # https://samtools.github.io/bcftools/bcftools-man.html#expressions
+# QUAL issue: https://github.com/tseemann/snippy/issues/228
 
 my $het_bp = 0;
 open my $het_fh, '-|',
-  qq{bcftools query -i 'GT="het"' -f '%CHROM\\t%POS\\t%REF\\n' $prefix.raw.vcf};
+  qq{bcftools query -i 'GT="het" || QUAL<$minqual' -f '%CHROM\\t%POS\\t%REF\\n' $prefix.raw.vcf};
 while (<$het_fh>) {
   chomp;
   my($chr,$pos,$ref) = split m/\t/;

perl5/Snippy/Version.pm

@@ -4,7 +4,7 @@ use base Exporter;
 @EXPORT_OK = qw(version);
 %EXPORT_TAGS = ( 'all' =>  [ @EXPORT_OK ] );
 
-our $VERSION = "4.0.7";
+our $VERSION = "4.1.0";
 
 use strict;
 use File::Basename;