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Option Type: FASFILE
Argument: cds preassembly seqin
Modules: extatic samphaser slimdip trex rje_samtools snapper
| Module | Option | Description | Default |
|---|---|---|---|
| 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.