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Alternative route
- Follow the Discover Variants Using SAM Tools (Workflow Tutorial) workflow (align reads -> Reformat file -> Identify variants -> Filter variants) to generate the filtered vcf files of background and F2 data set respectively
- DE App, SAMTOOLS-0.1.19_mpileup_raw-vcf-out, is recommended instead in the "Identify variants" step
- DE App, SAMTOOLS-0.1.19_VCF-Utilities_varFilter, is recommended instead in the " Filter variants" step
Filter the F2 SNPs against background SNPs and identify the SNPs induced by EMS via DE apps, EMS_mutation_filter, to get the final result
Info Please make sure the background and F2 filtered vcf files have different file names. If not, please rename one of them (the background filtered vcf file is recommended one, since it would be reused likely)
- In case that the same background data set is used in different analysis again, the filtered vcf of the same background data set could be used, no need to be regenerated
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Samtools, Bcftools, and Vcfutils
Discover Variants Using SAM Tools (Workflow Tutorial)
Integrated applications
iPlant validated workflow
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