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Appreci8 website  

Appreci8 is a variant calling pipeline for detecting single nucleotide variants (SNVs) and short indels (up to 30 bp) in next-generation sequencing (NGS) data. By integrating and filtering the output of eight individual variant calling tools on the basis of an artifact- and a polymorphism score, appreci8 succeeds in calling variants with high sensitivity and positive predictive value even at variant allele frequencies of 1 percent.

Environment Modules

Run module spider Appreci8 to find out what environment modules are available for this application.

System Variables

  • HPC_APPRECI8_DIR - installation directory
  • HPC_APPRECI8_BIN - executable directory

Additional Information

HiPerGator provides a "wrapper" to call the underlying container image. An example of the proper way to call the program would look something like:

  $ module load appreci8/20180530
  $ appreci8 /path/to/your/data/

where /path/to/you/data/ is a directory set up as follows (from the description at

The data you wish to analyze has to be prepared in the following way (compare folder Example contained in the appreci8 folder):
   SampleNames.txt: The names of the samples you wish to analyze (without file extension, one name per line)
   vcf_header.txt: Standard vcf file header (available in the appreci8 folder)
   Folder alignment: Containing the bam- and bai files of the samples you wish to analyze (format: sample1.bam, sample1.bai etc.)
   Folder snpEff_ann:
       Hotspots.txt: A list containing known hotspot mutations, covering Gene, Mutation (change on amino acid level, one-letter-code), Min_VAF (minimum allelic frequency at which you expect these mutations); an empty list can be passed, containing the header and three NA's (available in the appreci8 folder)
       transcripts.txt: A list containing the genes and the corresponding Ensembl transcript-IDs to be analyzed (without header; e.g. NRAS\tab ENST00000369535; for an example see file in the Example folder)
   Folder targetRegions:
       targetRegions.bed: Bed file containing the target regions to be analyzed (no header, no information except for chr, start, end; 1 instead of chr1 etc.; for an example see file in the Example folder)

An example of how to set up the analysis data folder can be found here