From 01bca3ba9e80fd875b7c0b7396b9e5871e50835c Mon Sep 17 00:00:00 2001 From: naumenko-sa Date: Tue, 5 Mar 2019 13:05:26 -0500 Subject: [PATCH] modified: README.md renamed: cre.roh.sh -> cre.roh.h3m2.sh renamed: cre.get_hom_stretch.sh -> cre.roh.naive.sh --- README.md | 3 +++ cre.roh.sh => cre.roh.h3m2.sh | 0 cre.get_hom_stretch.sh => cre.roh.naive.sh | 0 3 files changed, 3 insertions(+) rename cre.roh.sh => cre.roh.h3m2.sh (100%) rename cre.get_hom_stretch.sh => cre.roh.naive.sh (100%) diff --git a/README.md b/README.md index 7dbf2a5..3beadcb 100644 --- a/README.md +++ b/README.md @@ -155,6 +155,7 @@ vcf.platypus.getNV.sh ${family}-platypus-annotated-decomposed.vcf.gz * cre.coverage.bamstats05.sh - calculate coverage * cre.fixit.sh - fixes sample names * cre.gemini_load.sh loads vep-annotated vcf to gemini db. +* cre.get_hom_stretch.sh retrieves MAF<5% high quality variants from gemini.db and reports stretches of >9 HOM variants. * cre.gnomad_scores.R - download and parse gnomad scores. * cre.immunopanels.R - annotates CRE report with 6 immunopanels. * cre.kinship.R - to plot relatedness (kinship) diagram for a group of samples. Sometimes helps to detect and solve mislabelling. @@ -162,6 +163,8 @@ vcf.platypus.getNV.sh ${family}-platypus-annotated-decomposed.vcf.gz * cre.rtg.validate.sh - validates NA12878 calls vs genome in a bottle callset with RTG and a bed file * cre.sh - master script to produce variant reports from bcbio output * cre.topmed.R - pull variant frequency from TopMed having rs_id +* cre.roh.h3m2.sh: a robust method of ROH/LOH analysis with h3m2, calls variants, accounts for exonic regions, LD, plots picture. +* cre.roh.naive.sh: retrieves MAF<5% high quality variants from gemini.db and reports stretches of >9 HOM variants. * cre.vcf.has2dp.sh fixes input vcf file from HAS pipeline (Illumina, TCAG) filling DP field * omim.sh * orphanet.sh diff --git a/cre.roh.sh b/cre.roh.h3m2.sh similarity index 100% rename from cre.roh.sh rename to cre.roh.h3m2.sh diff --git a/cre.get_hom_stretch.sh b/cre.roh.naive.sh similarity index 100% rename from cre.get_hom_stretch.sh rename to cre.roh.naive.sh