java -jar ~/Trimmomatic-0.38/trimmomatic-0.38.jar SE -phred33 chr6.fastq chr6_tri.fastq SLIDINGWINDOW:10:28
fastqc chr6_tri.fastq
hisat2-build-l chr6.fasta file
hisat2 -x file -U chr6_tri.fastq --no-spliced-alignment --no-softclip > align.sam
samtools view align.sam -bo align.bam	
samtools sort align.bam -o sorted.bam
samtools index sorted.bam
samtools idxstats sorted.bam > totalread.txt
samtools mpileup sorted.bam > snp.bcf
bcftools call -cv snp.bcf -o snp.vcf