ngs-utils 17.10.2

• fix for inclusion phiX in exomes

• fix that duplicated regions will be merged in the bedfile

• new script that compares samples with heterozygotes to samples with ASE effect

ngs-utils 17.10.1

• updated countCoverage calculations
• updated prepare_ngs_bedfiles

17.09.1

• Added new scripts for:

  • reverting bam to FastQ
  • created a script for check the snps for validation of the ngs_dna pipeline

• expanded tortilla.sh with:

  • revertFromBamToFastQ
  • checkValidationNGS_DNA option

• updated bamout.sh, by default you will get all the reads of the region (with or without SNP calls in that region), there is an option to turn this off (e.g. big regions)

17.08.3: Merge pull request #166 from freerkvandijk/master

Added script to filter VCF file on call rate and genotype quality (pe…

17.08.2

Merge pull request #165 from pneerincx/master

Updates for PGx

17.08.1

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Created a wrapper for ngs tools called tortilla containing the following tools:

• countCoverage
• vcf-compare
• makeSamplesheet
• bamout

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• Added makeSamplesheet script

17.06.1

Added countcoverage script

ngs-utils 17.01.1

updated CreateIlluminaSampleSheet when there is only one barcode or 2 barcodes

ngs-utils 16.12.1

update demultiplexing when there is an unknown barcode

16.10.2

• vcf-compare_2.0 will now also accept vcf.gz files (auto-detect)
• wrapper script around prepare_NGS_bedfiles
• fix +1 base in making bedfiles