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Option Type: FASFILE

Argument: cds preassembly seqin

Modules: extatic samphaser slimdip trex rje_samtools snapper

ModuleOptionDescriptionDefault
extatic cds=FASFILE CDS input sequence file. (or cdsin=FASFILE) *.cds.fas based on cdna or singleseq
extatic seqin=FASFILE cDNA input seqence file (*.cdna.fas). See docs for naming advice. ExTATIC.cdna.fas
rje_samtools seqin=FASFILE Sequence file for loci in MPileup/SAM files (e.g. matching all relevant RID files) None
samphaser seqin=FASFILE Input genome to phase variants in
slimdip seqin=FASFILE File containing spoke protein sequences. If not found, will generate from SpokeUni field None
snapper seqin=FASFILE Input genome to identify variants in
trex preassembly=FASFILE Fasta file of preassembly reads
trex seqin=FASFILE Fasta file of representative repeat sequences for removal

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.