split haplotype caller by chromosome for all germline pipelines

CCBR · Sep 28, 2018 · 39f6ca3 · 39f6ca3
1 parent 3ac58f5
commit 39f6ca3
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Showing 3 changed files with 649 additions and 148 deletions.
diff --git a/Rules/all-wgslow.rl b/Rules/all-wgslow.rl
@@ -8,7 +8,7 @@ if config['project']['annotation'] == "hg19":
            "combined.strictFilter.vcf",
            "manta_out/results/variants/diploidSV.vcf.gz",
            config['project']['workpath']+"/svaba_out/svaba.log",
-           expand("{s}"+".g.vcf",s=samples),
+#           expand("{s}"+".g.vcf",s=samples),
            expand("canvas_out/{s}/CNV.vcf.gz", s=samples),
            "admixture_out/admixture_table.tsv",
            expand("{s}.recal.bam",s=samples),
@@ -39,7 +39,7 @@ elif config['project']['annotation'] == "hg38":
            "combined.strictFilter.vcf",
            "manta_out/results/variants/diploidSV.vcf.gz",
            config['project']['workpath']+"/svaba_out/svaba.log",
-           expand("{s}"+".g.vcf",s=samples),
+#           expand("{s}"+".g.vcf",s=samples),
            expand("canvas_out/{s}/CNV.vcf.gz", s=samples),
            "admixture_out/admixture_table.tsv",
            expand("{s}.recal.bam",s=samples),