Improvements
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Supports CRAM file write on queryname-based sorting. It auto-detects cram file extension on output file.
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Adds the following new options:
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--mutect-germline-resource -
--mutect-alleles -
--force-call-filtered-alleles
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Updates to match the baseline version v1.6.
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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.
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Better messaging in filehandle when reading index files to avoid user confusion.
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Better error checking when reading FASTQ files: checks that each FASTQ read name line starts with '@'.