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snp analysis in whole dna

hi I want DNA for snp data analysis .I do not have enough information in commands and software.which soft ware must be use for analysis in each step. i want commands for linux and R program. can i replace my data in general commands linux for analysis?If you help me I would be thankful commands for 1 quality control 2 alignment 3 variation

snp
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updated by Petr Ponomarenko Petr Ponomarenko • written by miravet65 • miravet65

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you might start with Broad Institute GATK Best Practices https://software.broadinstitute.org/gatk/best-practices/

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written by Petr Ponomarenko Petr Ponomarenko

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