add strand depth for gatk /issues/52

jodyphelan · Oct 14, 2024 · 104116c · 104116c
1 parent e44093e
commit 104116c
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diff --git a/pathogenprofiler/variant_calling.py b/pathogenprofiler/variant_calling.py
@@ -103,7 +103,7 @@ class GatkCaller(VariantCaller):
     def call_variants(self) -> Vcf:
         # Call variants using GATK
         if self.platform=="illumina":
-            self.calling_cmd = "samtools view -T %(ref_file)s -h %(bam_file)s {region} %(samclip_cmd)s | samtools view -b > %(temp_file_prefix)s.{region_safe}.tmp.bam && samtools index %(temp_file_prefix)s.{region_safe}.tmp.bam && gatk HaplotypeCaller -R %(ref_file)s -I %(temp_file_prefix)s.{region_safe}.tmp.bam -O /dev/stdout -L {region} %(calling_params)s -OVI false | bcftools norm -f %(ref_file)s -Oz -o %(temp_file_prefix)s.{region_safe}.vcf.gz" % vars(self)
+            self.calling_cmd = "samtools view -T %(ref_file)s -h %(bam_file)s {region} %(samclip_cmd)s | samtools view -b > %(temp_file_prefix)s.{region_safe}.tmp.bam && samtools index %(temp_file_prefix)s.{region_safe}.tmp.bam && gatk HaplotypeCaller -A StrandBiasBySample -R %(ref_file)s -I %(temp_file_prefix)s.{region_safe}.tmp.bam -O /dev/stdout -L {region} %(calling_params)s -OVI false | bcftools norm -f %(ref_file)s -Oz -o %(temp_file_prefix)s.{region_safe}.vcf.gz" % vars(self)
         else:
             raise NotImplementedError("%s not implemented for %s platform" % (self.__software__,self.platform))
         return self.run_calling(self.calling_cmd)

diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
@@ -20,6 +20,9 @@ def get_stand_support(var: pysam.VariantRecord,alt: str) -> Tuple[int,int]:
     elif 'ADF' in var.samples[0]:
         forward_support = var.samples[0]['ADF'][alt_index+1]
         reverse_support = var.samples[0]['ADR'][alt_index+1]
+    elif 'SB' in var.samples[0]:
+        forward_support = var.samples[0]['SB'][(alt_index+1)*2]
+        reverse_support = var.samples[0]['SB'][(alt_index+1)*2+1]
     else:
         forward_support = None
         reverse_support = None