[kevshaw@451]$ history
     1  w
     2  top
     3  w
     4  date
     5  mkdir sc
     6  cd sc
     7  wget ftp://ftp.ensembl.org/pub/current_fasta/saccharomyces_cerevisiae/dna/Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
     8  ls
     9  gzip -dv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa.gz
    10  ls -al
    11  less Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa
    12  mv Saccharomyces_cerevisiae.R64-1-1.dna_sm.toplevel.fa yeast.fa
    13  ls
    14  samtools -h
    15  samtools
    16  samtools faidx yeast.fa
    17  ls
    18  less yeast.fa.fai
    19  bwa index yeast.fa
    20  ls
    21  wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_1.fastq.gz
    22  ls
    23  ls -al
    24  gzip -dv SRR507778_1.fastq.gz
    25  less SRR507778_1.fastq
    26  cat SRR507778_1.fastq | wc -l
    27  bc
    28  wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR507/SRR507778/SRR507778_2.fastq.gz
    29  gzip -dv SRR507778_2.fastq.gz
    30  cat SRR507778_2.fastq | wc -l
    31  cat SRR507778_1.fastq | head -5000 > 1.fastq
    32  head -5000 SRR507778_2.fastq > 2.fastq
    33  cat 1.fastq | wc -l ; cat 2.fastq | wc -l
    34  ls
    35  bwa mem yeast.fa 1.fastq 2.fastq > yeast.sam
    36  less yeast.sam
    37  samtools sort -O bam -T . -I 0 -o yeast.bam yeast.sam
    38  samtools sort -O BAM -T . -l 0 -o yeast.bam yeast.sam
    39  ls
    40  less yeast.bam
    41  ls -al
    42  samtools view -T yeast.fa -C -o yeast.cram yeast.bam
    43  less yeast.cram
    44  samtools view yeast.cram | less
    45  samtools mpileup -f yeast.fa yeast.cram
    46  samtools mpileup -f yeast.fa yeast.cram | less
    47  bcftools mpileup -Ou f yeast.fa yeast.bam | bcftools call -vmO z -o snps.vcf.gz
    48  bcftools mpileup -Ou -f yeast.fa yeast.bam | bcftools call -vmO z -o snps.vcf.gz
    49  ls
    50  gzip -dv snps.vcf.gz
    51  less snps.vcf
    52  cd
[kevshaw@451]$