Print the alignment in the pileup format.
reference fasta file
output
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.pileup
output_bam
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.sorted
cap mapping quality at INT
any extra parameters
filtering reads with bits in INT
the input is in SAM
number of haplotypes in the sample (for -c/-g)
output the 2nd best call and quality
output in the GLFv3 format (suppressing -c/-i/-s)
output the maq consensus sequence
phred prob. of an indel in sequencing/prep. (for -c/-g)
print variants only (for -c)
phred prob. of an indel in sequencing/prep. (for -c/-g)
number of haplotypes in the sample (for -c/-g)
only show lines/consensus with indels
simple (yet incomplete) pileup format
number of haplotypes in the sample (for -c/-g)
use the SOAPsnp model for SNP calling