A utility that calculates statistics off a vcf stream, reporting at a given interval in json
Note: Please use the stable branch, as the master branch contains untested changes. Note: autoconf/autoheader must be installed in order to build htslib dependency Note: On linux systems, use 'sudo make' rather than 'make'. Also export LD_LIBRARY_PATH="/usr/local/lib" before running so that htslib can be found for dynamic loading.
vcfstatsalive [options] [vcf-file]
Options:
-u updateRate [default=1000] The number of reads vcfstatsalive needs to process before producing another statistics update
-f firstUpdateRate [default=0] The number of reads vcfstatsalive needs to process before producing the first statistics update. Useful to increase app responsiveness
-q qualHistLowerVal [default=1] The lower value of invalid QUAL value. Any QUAL value less than this will not be counted towards quality histogram
-Q qualHistUpperVal [default=200] The upper value of invalid QUAL value. Any QUAL value greater than this will not be counted towards quality histogram
-l logScaleAF [default=false] When specified, allele frequency histogram will be in log scale
-b batch [default=false] When specified, the statistics will only be outputed a single time at the end of the analysis.
If no vcf-file is specified, input is then read from stdin