get_stats_from_flagstat.pl: is used within the cleanup_Dx scripts (EXOME and GENOME) to calculate flagstats statistics.
folder ExomeDepth: contains the wrapper scripts for Exomedepth CNV analysis
see ExomeDepth/README.md for more information
folder ParseCNVQC: contains script to make summary of CNV QC's and send mail. Note: this tool is not for diagnostic use!
/GIAB_rtgtools/compare_vcf_to_giab_truth.pl: is used for GIAB comparisons: see GENOOM160
mips_fingerprint/coverage_mips.sh: is used for validation of new MIP pool, see GENOOM080 5.3.3
HGMD_preferred_transcript_Alissa/check_dxgenes_in_alissa.py: script to check if Alissa HGMD transcripts are present in the UMCU target BED file (i.e. used in Exoncov) Usage:\
python check_dxgenes_in_alissa.py {gene file} {Alissa HGMD file} {gene alias} > {output} {gene file} = list with all genes in the target BED file
{Alissa HGMD file} = tab seperated file with geneID and transcriptID
{gene alias} = tab seperated file with Alias_geneID and HGNC_approved_geneID