源码阅读网7月Netty成长课
校正测序错误和部分实验所致误差
#analyze patterns of covariation in the dataset
java -jar $GATK \
-T BaseRecalibrator \
-R $DB/hg19.fa \
-I dedup_sample1.bam \
-L chr22 \ # restrict analysis to only chromosome 22,名称参考前面hg19.dict文件
-knownSites $DB/dbsnp_138.hg19.vcf \
-knownSites $DB/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf \
-knownSites $DB/1000G_phase1.indels.hg19.sites.vcf \
-o recal_data_sample1.table
