call_snps_pipeline_v9.pl -r <reference_genome> [-nosnp T/F default F][-o <oligos_file>] [-R <parent/reference fastq prefix if any>] -S [skip mappings, just do SNP calls, defaulf = F] -D T/F [delete temp files default F] -f [-c chromosome_ID] -A <reference annotation [RH88/GT1/ME49/Pf3D7/ATH/BESB1 other path to file]>
Required parameters:
-r <reference_genome> Add reference genome in fasta format
-f File containing fastq file prefixes, one prefix per line.
Optional parameters:
-nosnp [T/F, default F] Just run read mapping withou calling SNPs/InDels
-o <oligos_file> Fasta file
-R <parent/reference fastq prefix if any> Use specified sample as the reference strain
-S [T/F, default F] Skip mappings, just do SNP calls.
-D [T/F, dafault F] Delete intermediate files generated by the pipeline.
-c chromosome_ID
-A [RH88|GT1|ME49|Pf3D7|ATH|BESB1|other path to file]
Figure 1: SNP calling pipeline scheme.
