bug fixes

naumenko-sa · Sep 10, 2018 · d005ab1 · d005ab1
1 parent 228aefe
commit d005ab1
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Showing 3 changed files with 2 additions and 7 deletions.
diff --git a/cre.bcbio.templates.annotate.yaml b/cre.bcbio.templates.annotate.yaml
@@ -19,16 +19,10 @@ details:
     - vep_splicesite_annotations
     - noalt_calling
     variantcaller: false
-#    - gatk-haplotype
-#    - samtools
-#    - platypus
-#    - freebayes
     vcfanno:
     - /home/naumenko/cre/cre.vcfanno.conf
   analysis: variant2
   description: [familyid]_sample
-#  files:
-#  - /hpf/largeprojects/ccmbio/naumenko/project_cheo/1171R/input/1171R_595742.bam
   vrn_file: ../input/[vrn_file]
   genome_build: GRCh37
   metadata:

diff --git a/cre.prepare_bcbio_run.sh b/cre.prepare_bcbio_run.sh
@@ -5,7 +5,7 @@ family=$1
 
 # $2 = template type,
 # - default = no value = default WES
-# - noalign - no alignment (for rerunning),
+# - noalign - no alignment (for rerunning or for running after alignment to reference with decoy),
 # - fast - no realignment,recalibration, and only gatk
 # - validation = NA12878 validation
 # - align_decoy - align only, reference with decoy

diff --git a/cre.roh.sh b/cre.roh.sh
@@ -7,6 +7,7 @@
 
 #ROH analysis with 
 #https://sourceforge.net/projects/h3m2/files/
+#https://www.ncbi.nlm.nih.gov/pubmed/24966365
 
 export H3M2PATH=/hpf/largeprojects/ccmbio/naumenko/tools/H3M2Tool