比对到参考基因组,生成SAM文件

bwa index -a bwtsw hg19.fa  #*.fa >2G,用-a bwtsw;*.fa < 2G，用-a is (默认）time bwa mem -M -t 10 -R '@RG\tID:HKV2KALXX.7\tSM:sample1\tPL:illumina\tLB:sample1' $DB/hg19.fa sample1_1.fq sample1_2.fq >aligned_sample1.sam#-M :Mark shorter split hits as secondary (essential for Picard compatibility)#-t: number of threads#-R:定义头文件,如果在此步骤不进行头文件定义，在后续GATK分析中还是需要重新增加头文件。具体信息可从样本的fq文件中获得。#@RG: Read Group，必须要有，否则GATK无法进行calling；比对速度比不加@RG更快  ##ID：Read group identifier, flowcell + lane name and number in Illunima data   >>>> ID:FLOWCELL1.LANE1(每个flowcell的每个lane是unique的), EX. HKV2KALXX.7#PL: platform>>> ILLUMINA#SM: Sample >>>sample1#LB: DNA preparation library identifier. MarkDuplicates uses the LB