Usage: biscuit cinread [options] <ref.fa> <in.bam>
Options:
-g STR Region (optional, will process the whole bam if not specified)
-t STR Target (c, cg, ch, hcg, gch, hch) [cg]
-p STR Content to print, ","-delimited: [QNAME,QPAIR,BSSTRAND,CRBASE,CQBASE]
Options + Descriptions:
QNAME: read name
QPAIR: which read in pair
STRAND: forward or reverse strand
BSSTRAND: which original strand the read derives from
MAPQ: MAPQ score
QBEG: read start position
QEND: read end position
CHRM: chromosome
CRPOS: cytosine position on reference
CGRPOS: CpG position on reference (-1 if not applicable)
CQPOS: cytosine position on read
CRBASE: cytosine reference base
CCTXT: cytosine context, strand flipped
CQBASE: base called on read
CRETENTION: retention (R) or conversion (C))
-s Consider secondary mapping [off]
-o STR Output file [stdout]
-h This help