[kevshaw@451]$ history
     1  ls
     2  cd seq
     3  ls
     4  rm *
     5  ls
     6  wget ftp://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  ls
    10  less yeast.fa
    11  samtools faidx yeast.fa
    12  sl
    13  ls
    14  less yeast.fa.fai
    15  bwa index yeast.fa
    16  ls
    17  wget https://yea4.us/451/data/SRR507778_1.fastq.gz
    18  wget https://yea4.us/451/data/SRR507778_2.fastq.gz
    19  ls
    20  gzip -dv *.gz
    21  ls
    22  less SRR507778_1.fastq
    23  history
    24  cat SRR507778_1.fastq | wc -l
    25  ls
    26  head -20000 SRR507778_1.fastq > 1.fastq
    27  head -20000 SRR507778_2.fastq > 2.fastq
    28  cat 1.fastq | wc -l
    29  bwa -h
    30  bwa
    31  bwa mem yeast.fa 1.fastq 2.fastq > yeast.sam
    32  less yeast.sam
    33  samtools sort -O BAM -T . -l 0 -o yeast.bam yeast.sam
    34  ls
    35  less yeast.bam
    36  history
    37  samtools view yeast.bam | less
    38  samtools view yeast.bam
    39  history
    40  samtools
    41  samtools | less
    42  samtools view -T yeast.fa -C -o yeast.cram yeast.bam
    43  less yeast.cram
    44  samtools mpileup -f yeast.fa yeast.cram | less
    45  bcftools mpileup -Ou -f yeast.fa yeast.bam | bcftools call -vmO z -o snps.vcf.gz
    46  ls
    47  gzip -dv snps.vcf.gz
    48  ls
    49  less snps.vcf
    50  cd
[kevshaw@451]$