prepare reference genome index

发表于 
1
2
3
4
5
6
7
8
# gatk
export JAVA_HOME=/home/wanglizhong/software/java/jre1.8.0_45; /ifshk4/BC_PUB/biosoft/PIPE_RD/Package/java/jre1.8.0_45/bin/java -Xmx5g -jar /home/wanglizhong/software/gatk/picard/picard.1.129.jar CreateSequenceDictionary R=UMD3.1.fasta O=UMD3.1.v3.dict
# samtools
samtools faidx UMD3.1.fasta
# bwa
bwa index -a bwtsw UMD3.1.fasta