Usage: biscuit pileup [options] <ref.fa> <in1.bam> [in2.bam in3.bam ...]
Som. Mode Usage: biscuit pileup [options] <-S -T tum.bam -I norm.bam> <ref.fa>
Options:
-g STR Region (optional, will process the whole bam if not specified)
-@ INT Number of threads [3]
-s INT Step of window dispatching [100000]
-N NOMe-seq mode [off]
-S Somatic mode, must provide -T and -I arguments [off]
-T STR Somatic mode, tumor BAM
-I STR Somatic mode, normal BAM
Output options:
-o STR Output file [stdout]
-w STR Pileup statistics output prefix [same as output]
-v INT Verbosity level (0: no added info printed, 0<INT<=5: print
diagnostic info, INT>5: print diagnostic and debug info) [0]
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 Maximum 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]
-r NO redistribution of ambiguous (Y/R) calls in SNP genotyping
-c NO filtering secondary mapping
-d Double count cytosines in overlapping mate reads (avoided
by default)
-u NO filtering of duplicate flagged reads
-p NO filtering of improper pair flagged reads
-n INT Maximum NM tag [999999]
Genotyping options:
-E FLOAT Error rate [0.001]
-M FLOAT Mutation rate [0.001]
-x FLOAT Somatic mutation rate [0.001]
-C FLOAT Contamination rate [0.010]
-P FLOAT Prior probability for heterozygous variant [0.333]
-Q FLOAT Prior probability for homozygous variant [0.333]
-h This help