Improvements
Supports CRAM file write on queryname-based sorting. It auto-detects cram file extension on output file.
Adds the following new options:
--mutect-germline-resource--mutect-alleles--force-call-filtered-alleles
Updates to match the baseline version v1.6.
Reduced reader buffer size to shorten the time it takes to start processing.
- fq2bamfast
Speed improvements.
Added support for BWA MEM options:
-B(values up to 15),-T,-L, and-U.Added support for reads longer than 500 bp using CPU recovery mode (note that speed will be slower and memory usage will be higher). Set
--max-read-lengthto the desired max read length for the FASTQ filter.
Better messaging in filehandle when reading index files to avoid user confusion.
Better error checking when reading FASTQ files: checks that each FASTQ read name line starts with '@'.