snp analysis in whole dna

Question

[miravet65]

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

Answer 1

[Petr Ponomarenko]

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