Created code to generate amended consensus without ambiguities but masked

svarona · svarona · commit 76d06f52bf77 · 2024-08-30T08:57:56.000+02:00
diff --git a/bu_isciii/templates/IRMA/DOC/irma_config.sh b/bu_isciii/templates/IRMA/DOC/irma_config.sh
@@ -5,3 +5,7 @@ MATCH_PROC=8		# grid maximum processes for the MATCH
 SORT_PROC=8		# currently not used
 ALIGN_PROC=8		# grid maximum processes for the rough align
 ASSEM_PROC=8		# grid maximum processes for assembly
+
+### AMENDED CONSENSUS ###
+MIN_AMBIG=0.75          # Sets ambiguities to off
+MIN_CONS_SUPPORT=9      # Mask low coverage <= 9 (10 is ok)
