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Workflow to discover and annotate SNPs and InDels from a collection of Illumina-based sequencing datasets

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SNP-calling-pipeline

Usage:

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. SNP_pipeline_scheme-9

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Workflow to discover and annotate SNPs and InDels from a collection of Illumina-based sequencing datasets

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