step1:grep data
step2:build index
Picard CreateSequenceDictionary creates .dict file and samtools faidx creates a .fai file. Both are needed for GATK
date bwa index t1.fa 2>t1.bwa.index.log && echo "bwa_indexs built" samtools faidx t1.fa 2>t1.samtools.faidx.log && echo "faidx built" java -jar /xxx/picard.jar CreateSequenceDictionary REFERENCE=t1.fa OUTPUT=t1.dict.new 2>picard.CreateSequenceDictionary.log && echo "dict built" date
step3:mapping
date bwa mem -t 4 -M ../02.index/t/t1.fa ../01.grep/t/o3.gz ../01.grep/t/o4.gz 2>bwa.mem.log |samtools view -bhS >t.bam 2>samtools.view.log && echo Bwa-mem-done date
step4:analyse
