[kevshaw@451]$ history
     1  w
     2  top
     3  w
     4  clear
     5  w
     6  cd seq/hs/
     7  ls
     8  less Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
     9  ls -al
    10  cd
    11  clear
    12  .holidaze/chanukah 60
    13  cd seq/
    14  ls
    15  rm snps.vcf
    16  rm *.bam
    17  rm *.cram
    18  rm *.amb
    19  rm *.ann
    20  rm yeast.fa.*
    21  ls
    22  rm yeast.sam
    23  ls
    24  less yeast.fa
    25  samtools faidx yeast.fa
    26  less yeast.fai
    27  less yeast.fa.fai
    28  bwa
    29  bwa index yeast.fa
    30  ls -al
    31  bwa mem yeast.fa 1.fastq 2.fastq
    32  ls
    33  bwa mem yeast.fa 1.fastq 2.fastq > yeast.sam
    34  less yeast.sam
    35  samtools sort -O BAM -T . -l 0 -o yeast.bam yeast.sam
    36  less yeast.bam
    37  w
    38  samtools view -T yeast.fa -C -o yeast.cram yeast.bam
    39  less yeast.cram
    40  samtools view yeast.cram | less
    41  bcftools mpileup -Ou -f yeast.fa yeast.bam | bcftools call -vmO z -o snps.vcf.gz
    42  gzip -d snps.vcf.gz
    43  less snps.vcf
    44  grep " INDEL" snps.vcf | wc -l
    45  grep " INDEL" snps.vcf
    46  grep "INDEL" snps.vcf
    47  grep "INDEL" snps.vcf | wc -l
    48  cd
[kevshaw@451]$