Merge branch 'refs/heads/master-priv' into master-pub

fritzsedlazeck · Nov 10, 2024 · f21b8ef · f21b8ef
2 parents f28e380 + 6a773b2
commit f21b8ef
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Showing 3 changed files with 9 additions and 9 deletions.
diff --git a/src/sniffles/genotyping.py b/src/sniffles/genotyping.py
@@ -135,7 +135,7 @@ def calculate(self):
 
         a, b = gt1
         svcall.genotypes[0] = (a, b, genotype_quality, coverage - support, support, self.phase)
-        svcall.set_info("AF", af)
+        svcall.set_info("VAF", af)
 
 
 class InsertionGenotyper(Genotyper):

diff --git a/src/sniffles/postprocessing.py b/src/sniffles/postprocessing.py
@@ -199,7 +199,7 @@ def qc_support_const(svcall, config):
 
 
 def qc_sv(svcall: SVCall, config: SnifflesConfig):
-    af = svcall.get_info("AF")
+    af = svcall.get_info("VAF")
     af = af if af is not None else 0
     sv_is_mosaic = af <= config.mosaic_af_max
 
@@ -368,7 +368,7 @@ def qc_sv(svcall: SVCall, config: SnifflesConfig):
 
 
 def qc_sv_post_annotate(svcall: SVCall, config: SnifflesConfig):
-    af = svcall.get_info("AF")
+    af = svcall.get_info("VAF")
     af = af if af is not None else 0
     sv_is_mosaic = af <= config.mosaic_af_max
 
@@ -389,10 +389,10 @@ def qc_sv_post_annotate(svcall: SVCall, config: SnifflesConfig):
 
     if config.mosaic:
         if sv_is_mosaic and (af < config.mosaic_af_min or af > config.mosaic_af_max):
-            svcall.filter = "MOSAIC_AF"
+            svcall.filter = "MOSAIC_VAF"
             return False
         elif not sv_is_mosaic and not config.mosaic_include_germline:
-            svcall.filter = "NOT_MOSAIC_AF"
+            svcall.filter = "NOT_MOSAIC_VAF"
             return False
 
     return True

diff --git a/src/sniffles/vcf.py b/src/sniffles/vcf.py
@@ -143,8 +143,8 @@ def write_header(self, contigs_lengths):
         self.write_header_line('FILTER=<ID=COV_CHANGE_FRAC_SC,Description="Coverage fractional change filter: start-center">')
         self.write_header_line('FILTER=<ID=COV_CHANGE_FRAC_CE,Description="Coverage fractional change filter: center-end">')
         self.write_header_line('FILTER=<ID=COV_CHANGE_FRAC_ED,Description="Coverage fractional change filter: end-downstream">')
-        self.write_header_line('FILTER=<ID=MOSAIC_AF,Description="Mosaic variant allele frequency filter">')
-        self.write_header_line('FILTER=<ID=NOT_MOSAIC_AF,Description="Variant allele frequency filter for non-mosaic">')
+        self.write_header_line('FILTER=<ID=MOSAIC_VAF,Description="Mosaic variant allele fraction filter">')
+        self.write_header_line('FILTER=<ID=NOT_MOSAIC_VAF,Description="Variant allele fraction filter for non-mosaic">')
         self.write_header_line('FILTER=<ID=ALN_NM,Description="Length adjusted mismatch filter">')
         self.write_header_line('FILTER=<ID=STRAND_BND,Description="Strand support filter for BNDs">')
         self.write_header_line('FILTER=<ID=STRAND,Description="Strand support filter for germline SVs">')
@@ -171,7 +171,7 @@ def write_header(self, contigs_lengths):
         self.write_header_line('INFO=<ID=SUPP_VEC,Number=1,Type=String,Description="List of read support for all samples">')
         self.write_header_line('INFO=<ID=CONSENSUS_SUPPORT,Number=1,Type=Integer,Description="Number of reads that support the generated insertion (INS) consensus sequence">')
         self.write_header_line('INFO=<ID=RNAMES,Number=.,Type=String,Description="Names of supporting reads (if enabled with --output-rnames)">')
-        self.write_header_line('INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">')
+        self.write_header_line('INFO=<ID=VAF,Number=1,Type=Float,Description="Variant Allele Fraction">')
         self.write_header_line('INFO=<ID=NM,Number=.,Type=Float,Description="Mean number of query alignment length adjusted mismatches of supporting reads">')
         self.write_header_line('INFO=<ID=PHASE,Number=.,Type=String,Description="Phasing information derived from supporting reads, represented as list of: HAPLOTYPE,PHASESET,HAPLOTYPE_SUPPORT,PHASESET_SUPPORT,HAPLOTYPE_FILTER,PHASESET_FILTER">')
 
@@ -249,7 +249,7 @@ def write_call(self, call):
             infos["END"] = end - 1
 
         infos_ordered = ["PRECISE" if call.precise else "IMPRECISE"]
-        af = call.get_info("AF")
+        af = call.get_info("VAF")
         af = af if af is not None else 0
         sv_is_mosaic = af <= self.config.mosaic_af_max
         if sv_is_mosaic and self.config.mosaic: