diff --git a/.gitignore b/.gitignore
index 0a89648..b083be6 100755
--- a/.gitignore
+++ b/.gitignore
@@ -31,3 +31,7 @@ tags_sorted_by_file
 *.sublime-project
 *.sublime-workspace
 Thumbs.db
+/bin
+/lib
+/include
+/nbproject
\ No newline at end of file
diff --git a/src/c++/lib/variant/VariantReader.cpp b/src/c++/lib/variant/VariantReader.cpp
index 0a1cc76..ae7067d 100755
--- a/src/c++/lib/variant/VariantReader.cpp
+++ b/src/c++/lib/variant/VariantReader.cpp
@@ -591,6 +591,44 @@ bool VariantReader::advance()
 
         ++ncalls;
         bcf_unpack(line, BCF_UN_ALL);
+        
+        std::string fmt_strings = bcfhelpers::getFormatString(reader.header, line, "FT", isample, "");
+        std::vector<std::string> fmt_filters;
+        stringutil::split(fmt_strings, fmt_filters, ";", false);
+        for(auto const & f : fmt_filters) 
+        {
+            if(f.empty() || f == "PASS") 
+            {
+                continue;
+            }
+            fail = true;
+            bool has_filter = false;
+            for(size_t ff = 0; ff < vars.calls[sid].nfilter; ++ff)
+            {
+                if(f == vars.calls[sid].filter[ff])
+                {
+                    has_filter = true;
+                    break;
+                }
+            }
+            if(!has_filter)
+            {
+                if(vars.calls[sid].nfilter + 1 > MAX_FILTER)
+                {
+                    error("Too many filters at %s:%i in sample %i", vars.chr.c_str(), vars.pos, sid);
+                }
+                vars.calls[sid].filter[vars.calls[sid].nfilter - 1] = f;
+                vars.calls[sid].nfilter++;
+            }
+        }
+
+        if(getApplyFilters((int) sid) && fail)
+        {
+            vars.calls[sid].ngt = 0;
+            vars.calls[sid].phased = false;
+            vars.calls[sid].nfilter = 0;
+            continue;
+        }
 
         vars.calls[sid].qual = line->qual;
 
diff --git a/src/c++/main/vcfcheck.cpp b/src/c++/main/vcfcheck.cpp
index 820a7bf..20adee6 100755
--- a/src/c++/main/vcfcheck.cpp
+++ b/src/c++/main/vcfcheck.cpp
@@ -353,6 +353,11 @@ int main(int argc, char *argv[])
                 {
                     if(gt[g] > 0)
                     {
+                        if(gt[g] + 1 > line->n_allele)
+                        {
+                            error("Call with invalid genotype (non-existent allele) at %s:%i", 
+                                  vchr.c_str(), vstart + 1);
+                        }
                         const char * alt = line->d.allele[gt[g]];
 
                         if(strchr(alt, '.') && strlen(alt) > 1)
diff --git a/src/data/faulty_gt.vcf b/src/data/faulty_gt.vcf
new file mode 100755
index 0000000..534a595
--- /dev/null
+++ b/src/data/faulty_gt.vcf
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.1
+##contig=<ID=chrQ,length=37>
+##INFO=<ID=END,Number=1,Type=Integer,Description="Variant end">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12877
+chrQ	1	.	A	.	.	PASS	.	GT	0/1
+chrQ	2	.	A	T	.	PASS	.	GT	0/2
diff --git a/src/data/faulty_gt.vcf.gz b/src/data/faulty_gt.vcf.gz
new file mode 100644
index 0000000..1671a37
Binary files /dev/null and b/src/data/faulty_gt.vcf.gz differ
diff --git a/src/data/faulty_gt.vcf.gz.tbi b/src/data/faulty_gt.vcf.gz.tbi
new file mode 100644
index 0000000..a7e74cf
Binary files /dev/null and b/src/data/faulty_gt.vcf.gz.tbi differ
diff --git a/src/data/per_sample_ft_lhs.vcf b/src/data/per_sample_ft_lhs.vcf
new file mode 100755
index 0000000..7ca2873
--- /dev/null
+++ b/src/data/per_sample_ft_lhs.vcf
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.1
+##contig=<ID=chrQ,length=37>
+##INFO=<ID=END,Number=1,Type=Integer,Description="Variant end">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12877
+chrQ	1	.	A	G	.	PASS	.	GT	0/1
+chrQ	2	.	A	T	.	PASS	.	GT	0/1
+chrQ	3	.	A	T	.	PASS	.	GT	0/1
diff --git a/src/data/per_sample_ft_rhs.vcf b/src/data/per_sample_ft_rhs.vcf
new file mode 100755
index 0000000..c8225ca
--- /dev/null
+++ b/src/data/per_sample_ft_rhs.vcf
@@ -0,0 +1,12 @@
+##fileformat=VCFv4.1
+##contig=<ID=chrQ,length=37>
+##INFO=<ID=END,Number=1,Type=Integer,Description="Variant end">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample filter">
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=A,Description="Filter A">
+##FILTER=<ID=B,Description="Filter B">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12877
+chrQ	1	.	A	G	.	PASS	.	GT	0/1
+chrQ	2	.	A	T	.	PASS	.	GT:FT	0/1:A
+chrQ	3	.	A	T	.	PASS	.	GT:FT	0/1:A;B