4.24. capsim: Simulating the Dynamics of Targeted Capture Sequencing with CapSim¶
capsim (jsa.sim.capsim) is a tool to simulate target capture sequencing. Its simulates the dynamics of capture process
4.24.1. Synopsis¶
jsa.sim.capsim: Simulate capture sequencing
4.24.2. Usage¶
jsa.sim.capsim [options]
4.24.3. Options¶
--reference=s Name of genome to be (REQUIRED) --probe=s File containing probes mapped to the reference in bam format (default=’null’) --logFile=s Log file (default=’-‘) --ID=s A unique ID for the data set (default=’‘) --miseq=s Name of read file if miseq is simulated (default=’null’) --pacbio=s Name of read file if pacbio is simulated (default=’null’) --fmedian=i Median of fragment size at shearing (default=‘2000’) --fshape=d Shape parameter of the fragment size distribution (default=‘6.0’) --smedian=i Median of fragment size distribution (default=‘1300’) --sshape=d Shape parameter of the fragment size distribution (default=‘6.0’) --tmedian=i Median of target fragment size (the fragment size of the data). If specified, will override fmedian and smedian. Othersise will be estimated (default=‘0’) --tshape=d Shape parameter of the effective fragment size distribution (default=‘0.0’) --num=i Number of fragments (default=‘1000000’) --pblen=i PacBio: Average (polymerase) read length (default=‘30000’) --illen=i Illumina: read length (default=‘300’) --ilmode=s Illumina: Sequencing mode: pe = paired-end, mp=mate-paired and se=singled-end (default=’pe’) --seed=i Random seed, 0 for a random seed (default=‘0’) --help Display this usage and exit (default=’false’)