Usage: biscuit epiread [options] <ref.fa> <in.bam>
Options:
-B STR Bed input for SNP display in epiread output
-g STR Region (optional, will process the whole bam if not specified)
-s STR Step of window dispatching [100000]
-@ INT Number of threads [3]
Output options:
-o STR Output file [stdout]
-N NOMe-seq mode [off]
-L INT maximum read length (will need to be increased for long reads) [302]
-M BAM file has modBAM tags (MM/ML) [off]
-P Pairwise mode [off]
-O Old BISCUIT epiread format, not compatible with -P [off]
-A Print all CpG and SNP locations in location column, ignored if -O not given [off]
-v Verbose (print additional info for diagnostics) [off]
Filter options:
-b INT Minimum base quality [20]
-m INT Minimum mapping quality [40]
-a INT Minimum alignment score (from AS-tag) [40]
-t INT Max cytosine retention in a read [999999]
-l INT Minimum read length [10]
-5 INT Minimum distance to 5' end of a read [3]
-3 INT Minimum distance to 3' end of a read [3]
-E NO filtering of empty epireads
-d Double count cytosines in overlapping mate reads (avoided
by default)
-u NO filtering of duplicate
-p NO filtering of improper pair
-n INT Maximum NM tag [999999]
-y FLT Minimum probability a modification is correct (0.0 - 1.0) [0.900000]
-h This help
Note, the -O (old epiread format) and -P (pairwise format for biscuit asm) are not guaranteed
to match output from biscuit pileup. These file formats have been left in for legacy purposes.
Default output with an unfiltered BISCUIT SNP BED file (biscuit pileup ...
-> biscuit vcf2bed -t snp ...) should have the same results in the epiBED as in pileup.