fix: split variants into biallelics

RIVM-bioinformatics · Jul 1, 2024 · be3c319 · be3c319
1 parent 3155e48
commit be3c319
Showing 1 changed file with 34 additions and 8 deletions.
diff --git a/workflow/rules/variant_filtering.smk b/workflow/rules/variant_filtering.smk
@@ -28,13 +28,39 @@ gatk FilterMutectCalls -V {input.vcf} \
 --microbial-mode 2>&1>{log}
         """
 
+rule split_multiallelic:
+    input:
+        vcf=OUT + "/variants_raw/FMC/{sample}.vcf",
+        ref=OUT + "/reference/reference.fasta",
+    output:
+        vcf=OUT + "/variants_raw/FMC_biallelic/{sample}.vcf",
+    message:
+        "Splitting multiallelic records into biallelic"
+    container:
+        "docker://staphb/bcftools:1.16"
+    conda:
+        "../envs/bcftools.yaml"
+    log:
+        OUT + "/log/split_multiallelic/{sample}.log",
+    threads: config["threads"]["filter_variants"]
+    resources:
+        mem_gb=config["mem_gb"]["filter_variants"],
+    shell:
+        """
+bcftools norm \
+--multiallelics - \
+--fasta-ref {input.ref} \
+{input.vcf} \
+1>{output.vcf} \
+2>{log}
+        """
 
 rule hard_filter_af:
     input:
-        vcf=OUT + "/variants_raw/FMC/{sample}.vcf",
+        vcf=OUT + "/variants_raw/FMC_biallelic/{sample}.vcf",
         ref=OUT + "/reference/reference.fasta",
     output:
-        vcf=OUT + "/variants_raw/FMC_afhard/{sample}.vcf",
+        vcf=OUT + "/variants_raw/FMC_biallelic_afhard/{sample}.vcf",
     message:
         "Hard filtering variants with very low allele frequency for {wildcards.sample}"
     container:
@@ -60,10 +86,10 @@ bcftools filter \
 
 rule soft_filter_af:
     input:
-        vcf=OUT + "/variants_raw/FMC_afhard/{sample}.vcf",
+        vcf=OUT + "/variants_raw/FMC_biallelic_afhard/{sample}.vcf",
         ref=OUT + "/reference/reference.fasta",
     output:
-        vcf=OUT + "/variants_raw/FMC_afhard_afsoft/{sample}.vcf",
+        vcf=OUT + "/variants_raw/FMC_biallelic_afhard_afsoft/{sample}.vcf",
     message:
         "Marking minority variants for {wildcards.sample}"
     container:
@@ -90,10 +116,10 @@ bcftools filter \
 
 rule filter_depth:
     input:
-        vcf=OUT + "/variants_raw/FMC_afhard_afsoft/{sample}.vcf",
+        vcf=OUT + "/variants_raw/FMC_biallelic_afhard_afsoft/{sample}.vcf",
         ref=OUT + "/reference/reference.fasta",
     output:
-        vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth/{sample}.vcf",
+        vcf=OUT + "/variants_raw/FMC_biallelic_afhard_afsoft_depth/{sample}.vcf",
     container:
         "docker://staphb/bcftools:1.16"
     conda:
@@ -131,7 +157,7 @@ if config["disable_mask"] == "True":
 
     rule filter_mask:
         input:
-            vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth/{sample}.vcf",
+            vcf=OUT + "/variants_raw/FMC_biallelic_afhard_afsoft_depth/{sample}.vcf",
             ref=OUT + "/reference/reference.fasta",
             mask=OUT + "/variants_raw/no_mask.bed",
         output:
@@ -163,7 +189,7 @@ else:
 
     rule filter_mask:
         input:
-            vcf=OUT + "/variants_raw/FMC_afhard_afsoft_depth/{sample}.vcf",
+            vcf=OUT + "/variants_raw/FMC_biallelic_afhard_afsoft_depth/{sample}.vcf",
             ref=OUT + "/reference/reference.fasta",
             mask=OUT + "/variants_raw/mask.bed",
         output: