modified: README.md

	modified:   cheo.R
	modified:   cre.gnomad_scores.R
	modified:   cre.panel_filter.R

README.md

@@ -149,14 +149,16 @@ vcf.platypus.getNV.sh ${family}-platypus-annotated-decomposed.vcf.gz
 * bcbio.array.pbs
 * bcbio.pbs
 * bcbio.prepare_families.sh
-* cre.prepare_bcbio_run.sh
 * bcbio.rename_old_names.sh
 * bcl2fastq.sh
+* cheo.R - mostly Venn diagrams to compare pipeline validations + some coverage analysis
+* cre.prepare_bcbio_run.sh
 * cre.bam.validate.sh
 * cre.bcbio.upgrade.sh
 * cre.coverage.bamstats05.sh - calculate coverage
 * cre.fixit.sh - fixes sample names
 * cre.gemini_load.sh loads vep-annotated vcf to gemini db.
+* cre.gnomad_scores.R - download and parse gnomad scores.
 * cre.kinship.R - to plot relatedness (kinship) diagram for a group of samples. Sometimes helps to detect and solve mislabelling.
 * cre.package.sh
 * cre.rtg.validate.sh - validates NA12878 calls vs genome in a bottle callset with RTG and a bed file