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See also `samtools flags` [0] -F, —filtering-flag STR|INT Filtering flag, 0 for unset. Note that some options only work on some file formats and only on read or write streams. If value is unspecified for a boolean option, the value is assumed to be 1. The valid options are as follows. nthreads=INT Specifies the number of threads to use during encoding and/or decoding. The authors wish to thank the medical technicians of the Veterinary Central laboratory, Department of Veterinary Clinical Sciences for performing the manual differential counts of the routine samples. The file can be optionally compressed by bgzip. [null] -G, —exclude-RG FILE Exclude reads from readgroups listed in FILE (one @RG-ID per line) -l, —positions FILE BED or position list file containing a list of regions or sites where pileup or BCF should be generated. Reducing INT leads to longer indels. [20] -F, —gap-frac FLOAT Minimum fraction of gapped reads [0.002] -h, —tandem-qual INT Coefficient for modeling homopolymer errors. This can be either a list of directories or URLs. Note that if a URL is included then the colon in and ftp:// and the optional port number will be treated as part of the URL and not a PATH field separator.

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