call snp教程:https://gencore.bio.nyu.edu/variant-calling-pipeline-gatk4/
参考基因组索引:
bwa index Genome.fasta
java -jar /home/jpf/biosoft/picard/picard.jar CreateSequenceDictionary R=/data2/tmp/my_snakemake/refgenome/GCA_009078335.1_ASM907833v1_genomic.fna O=/data2/tmp/my_snakemake/refgenome/GCA_009078335.1_ASM907833v1_genomic.dict
samtools faidx /data2/tmp/my_snakemake/refgenome/GCA_009078335.1_ASM907833v1_genomic.fna