From 354f5da90f8d3689b306153e0473a8b053e3bbbb Mon Sep 17 00:00:00 2001
From: naumenko-sa <evolgenomicslab@gmail.com>
Date: Thu, 25 Oct 2018 12:28:32 -0400
Subject: [PATCH] 	modified:   README.md 	modified:   cre.vcf.has2dp.sh

---
 README.md         | 1 +
 cre.vcf.has2dp.sh | 1 +
 2 files changed, 2 insertions(+)

diff --git a/README.md b/README.md
index e5f29f8..3b8f53c 100644
--- a/README.md
+++ b/README.md
@@ -164,6 +164,7 @@ vcf.platypus.getNV.sh ${family}-platypus-annotated-decomposed.vcf.gz
 * cre.gemini_load.sh loads vep-annotated vcf to gemini db.
 * cre.package.sh
 * cre.sh
+* cre.vcf.has2dp.sh fixes input vcf file from HAS pipeline (Illumina, TCAG) filling DP field
 * gemini.gemini2txt.sh
 * gemini.refseq.sh
 * gemini.variant_impacts.sh
diff --git a/cre.vcf.has2dp.sh b/cre.vcf.has2dp.sh
index a5db8d8..6375104 100755
--- a/cre.vcf.has2dp.sh
+++ b/cre.vcf.has2dp.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
 # if input vcf is from TCAG (HAS) it does not have DP INFO field, we need to fake it from FORMAT DP for SNVs and from DPI for indels:
+# don't forget to change sample name if necessary with bcftools reheader
 
 bname=`basename $1 .vcf.gz`