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`