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