Adding regions file to WES mk_examples command to speed up run time

Author: skchronicles

workflow/rules/germline.smk

@@ -31,6 +31,7 @@ rule deepvariant_make_examples:
     input: 
         bam = join(workpath, "BAM", "{name}.sorted.bam"),
         bai = join(workpath, "BAM", "{name}.sorted.bam.bai"),
+        bed = provided(join(workpath, "references", "wes_regions_50bp_padded.bed"), run_wes),
     output:
         success = join(workpath, "deepvariant", "mk_examples", "{name}.make_examples.success"),
     params: 
@@ -46,7 +47,11 @@ rule deepvariant_make_examples:
             w.name,
             int(allocated("threads", "deepvariant_make_examples", cluster))
         )),
-    message: "Running DeepVariant make_examples on '{input.bam}' input file"
+        # Call variants within regions BED 
+        # file created from WES capture kit
+        wes_region_option = lambda _: "--regions {0}".format(
+            join(workpath, "references", "wes_regions_50bp_padded.bed"),
+        ) if run_wes else '',
     threads: int(allocated("threads", "deepvariant_make_examples", cluster))
     container: config['images']['deepvariant']
     envmodules: config['tools']['deepvariant']
@@ -74,7 +79,7 @@ rule deepvariant_make_examples:
             --halt 2 \\
             --line-buffer \\
             make_examples \\
-                --mode calling \\
+                --mode calling {params.wes_region_option} \\
                 --ref {params.genome} \\
                 --reads {input.bam} \\
                 --examples {params.example} \\
@@ -131,7 +136,6 @@ rule deepvariant_call_variants:
         #  @WES = "/opt/models/wes/model.ckpt"
         #  @WGS = "/opt/models/wgs/model.ckpt"
         ckpt = lambda _: "/opt/models/wes/model.ckpt" if run_wes else "/opt/models/wgs/model.ckpt",
-    message: "Running DeepVariant call_variants on '{wildcards.name}' sample"
     threads: int(allocated("threads", "deepvariant_call_variants", cluster))
     container: config['images']['deepvariant']
     envmodules: config['tools']['deepvariant']
@@ -197,7 +201,6 @@ rule deepvariant_postprocess_variants:
             w.name,
             int(allocated("threads", "deepvariant_make_examples", cluster))
         )),
-    message: "Running DeepVariant postprocess_variants on '{input.callvar}' input file"
     threads: int(allocated("threads", "deepvariant_postprocess_variants", cluster))
     container: config['images']['deepvariant']
     envmodules: config['tools']['deepvariant']

workflow/rules/somatic.smk

@@ -630,8 +630,9 @@ rule hmftools_sage:
     data using the same set of options for WGS. At the current moment, sage
     does not have an option to restrict variant calling to specific regions.
     It does have an -high_depth_mode option; however, the authors state it 
-    should only be used for small targeted panels. For more information 
-    about hmftools visit github:
+    should only be used for small targeted panels. In the 'somatic_selectvar'
+    rule, any variants outside the padded regions/capture-kit BED file are
+    removed in WES data. For more information about hmftools visit github:
     https://github.com/hartwigmedical/hmftools
     @Input:
         Sorted BAM file (scatter-per-tumor-sample)
@@ -796,6 +797,11 @@ rule deepsomatic_make_examples:
         #  @WES = "/opt/models/deepsomatic/wes"
         #  @WGS = "/opt/models/deepsomatic/wgs"
         ckpt = lambda _: "/opt/models/deepsomatic/wes" if run_wes else "/opt/models/deepsomatic/wgs",
+        # Call variants within regions BED 
+        # file created from WES capture kit
+        wes_region_option = lambda _: "--regions {0}".format(
+            join(workpath, "references", "wes_regions_50bp_padded.bed"),
+        ) if run_wes else '',
         # Get tumor and normal sample names 
         tumor  = '{name}',
         # Building option for the paired normal sorted bam
@@ -848,7 +854,7 @@ rule deepsomatic_make_examples:
                 --reads_tumor {input.tumor}  {params.normal_bam_option} \\
                 --sample_name_tumor {params.tumor} {params.normal_name_option} \\
                 --examples {params.example} \\
-                --checkpoint "{params.ckpt}" \\
+                --checkpoint "{params.ckpt}" {params.wes_region_option} \\
                 --vsc_max_fraction_indels_for_non_target_sample "0.5" \\
                 --vsc_max_fraction_snps_for_non_target_sample "0.5" \\
                 --vsc_min_fraction_indels "0.05" \\
@@ -1337,7 +1343,8 @@ rule somatic_selectvar:
     somatic callers. This step takes the somatic calls from all the callers
     (assumes already re-headered if needed, i.e. strelka and muse), and then 
     runs bcftools norm to split multi-allelic sites AND gatk SelectVariants 
-    to filter sites.
+    to filter sites. For WES data, this step will also remove any variants
+    that are outside the padded regions/capture-kit BED file.
     @Input:
         Per sample, per caller, VCF somatic variants
     @Output: