源碼閱讀網7月Netty成長課
校正測序錯誤和部分實驗所致誤差
#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,名稱參考前面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
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