[kevshaw@451]$ history
     1  date
     2  cd seq
     3  ls
     4  rm -rf *
     5  ls
     6  wget http://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
     7  gzip -dv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
     8  mv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa yeast.fa
     9  samtools faidx yeast.fa
    10  less yeast.fai
    11  ls
    12  less yeast.fa.fai
    13  less yeast.fa
    14  history
    15  bwa index yeast.fa
    16  wget https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_1.fastq.gz
    17  wget https://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_2.fastq.gz
    18  ls
    19  gzip -dv *.gz
    20  head -20000 SRR507778_1.fastq > 1.fastq
    21  head -20000 SRR507778_2.fastq > 2.fastq
    22  ls
    23  bwa mem yeast.fa 1.fastq 2.fastq > yeast.sam
    24  ls
    25  less yeast.sam
    26  samtools sort -O BAM -T . -l 0 -o yeast.bam
    27  samtools sort -O BAM -T . -l 0 -o yeast.bam yeast.sam
    28  ls
    29  less yeast.bam
    30  cat yeast.bam
    31  q
    32  ls
    33  samtools view yeast.bam | less
    34  samtools view -T yeast.fa -C -o yeast.cram yeast.bam
    35  samtools mpileup -f yeast.fa yeast.cram | less
    36  bcftools mpileup -Ou -f yeast.fa yeast.bam | bcftools call -vmO z -o snps.vcf.gz
    37  less snps.vcf.gz
    38  bwa mem yeast.fa SRR507778_1.fastq SRR507778_2.fastq > yeast.sam
    39  top
    40  cd
[kevshaw@451]$