Call SNVs with respect to the reference sequence

cbg-ethz · May 18, 2020 · c94f299 · c94f299
1 parent b43d350
commit c94f299
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/rules/common.smk b/rules/common.smk
@@ -211,6 +211,7 @@ class VpipeConfig(object):
             'threads': __RECORD__(value=0, type=int),
             'conda': __RECORD__(value='', type=str),
 
+            'consensus': __RECORD__(value=True, type=bool),
             'alpha': __RECORD__(value=0.1, type=float),
             'ignore_indels': __RECORD__(value=False, type=bool),
             'coverage': __RECORD__(value=0, type=int),
@@ -227,6 +228,7 @@ class VpipeConfig(object):
             'time': __RECORD__(value=60, type=int),
             'conda': __RECORD__(value='', type=str),
 
+            'consensus': __RECORD__(value=True, type=bool),
             'extra': __RECORD__(value='', type=str),
         }),
         ('alignment_coverage', {

diff --git a/rules/snv.smk b/rules/snv.smk
@@ -99,10 +99,9 @@ def read_len(wildcards):
     read_len = patient_dict[patient_tuple]
     return read_len
 
-
 rule snv:
     input:
-        REF = "variants/cohort_consensus.fasta",
+        REF = "variants/cohort_consensus.fasta" if config.snv['consensus'] else reference_file,
         BAM = "{dataset}/alignments/REF_aln.bam",
         TSV = "{dataset}/variants/coverage_intervals.tsv",
     output:
@@ -233,7 +232,7 @@ rule samtools_index:
 
 rule lofreq:
     input:
-        REF = "variants/cohort_consensus.fasta",
+        REF = "variants/cohort_consensus.fasta" if config.lofreq['consensus'] else reference_file,
         REF_IDX = "variants/cohort_consensus.fasta.fai",
         BAM = "{dataset}/alignments/REF_aln.bam",
     output: