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全外显子分析（WES）的一般步骤-1
其实很多步骤网上基本都有，现在生物信息学已经没有十年前那么神秘了，流程基本自动化，标准化分析一个全外显子，已经从十年前的几千块钱，狂跌至现在的几十块钱了。
基本步骤包括这些：其中1是配置，2-11都是比对校正。12-14是统计，15是去除杂的中间产物，节省空间。 16-18是call出SNP， 后面几步是注释。 1. Global config : Set up global configuration of the pipeline. 2. Mapping : Align short sequences to the human reference genome sequence database. 3. Fixmate : Fixing the mate pairs information to ensure that all mate-pair information is in sync between each read and it's mate pair. 4. Filter : Filtering for mapping, pairing, and proper paired 5. Remove duplicate : Examines aligned records in the BAM file to locate duplicate reads and remove them. 6. Filter low mapping quality : Filter low mapping quality reads 7. Create intervals : Collect regions around potential indels and clusters of mismatches. Determine small suspicious intervals which are likely in need of realignment. 8. Realignment : Run the realigner over the intervals to create a cleaned version of the BAM file. 9. Analysis of covariates : Determine the covariates affecting base quality scores in the BAM file. 10. Recalibration : Walking through the BAM file and rewrite the quality scores. 11. Recalculate analysis of covariates : Determine the covariates affecting base quality scores in the realigned recalibrated BAM file for the comparison. 12. Depth of coverage : Determine coverage summarized by mean, median, quartiles, and/or percentage of bases covered. 13. DoC for genes : Determine coverage on genes 14. HsMetrics : Calculates a set of Hybrid Selection specific metrics from an aligned BAM file.. 15. Cleanup : Remove all intermediate alignment and BAM files. Keep only first aligned and last realigned-recalibrated BAM files. 16. Calling variants a) Generate snps raw vcf file b) Generate indels raw vcf file c) Variant filtration generate indels and indels.PASS files d) Variant filtration generate snps and snps.PASS files e) evaluating snps 17. Group Calling and Variant Recalibration a) UnifiedGenotyper Group Calling b) Variant Recalibration c) Apply Recalibration d) Variant_Evaluation 18. Generate genotype 19. Annotation snpEff 20. Annotation Annovar |
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