Merge pull request #103 from sanjaynagi/change-min-alternate-fraction…

…-freebayes-19-07-24 freebayes add parameter: min-alternate-fraction 0.05
sanjaynagi · Jul 19, 2024 · 6638816 · 6638816
2 parents 69fe338 + 6e3af41
commit 6638816
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflow/rules/hisat2-freebayes.smk b/workflow/rules/hisat2-freebayes.smk
@@ -96,7 +96,7 @@ rule VariantCallingFreebayes:
         "../envs/variants.yaml"
     threads: 1
     shell:
-        "freebayes -f {input.ref} -t {input.regions} --ploidy {params.ploidy} --populations {input.pops} --pooled-discrete --use-best-n-alleles 5 -L {input.samples} > {output} 2> {log}"
+        "freebayes -f {input.ref} -t {input.regions} --ploidy {params.ploidy} --populations {input.pops} --pooled-discrete --use-best-n-alleles 5 --min-alternate-fraction 0.05 -L {input.samples} > {output} 2> {log}"
 
 chunks = np.arange(1, config["VariantAnalysis"]["chunks"])