modified: README.md

modified: cre.vcf.has2dp.sh
naumenko-sa · Oct 25, 2018 · 354f5da · 354f5da
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diff --git 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
@@ -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`