Page Comparison

...

Tuesday Nov. 13th

• Results of variant calling
• SNP Annotation
• Reference databasesReview NGS - from cellular DNA to variant data
• Review results of variant calling - for these examples, Start IGV, load the genome, "Human (1kg, b37+)", load the three NA*.bam files (the corresponding *.bai must exist in the same directory).

  Code Block
  title Command to view the contents of a sorted (by genome coordinates) BAM file
  samtools view NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | head

  Examine the first read of the file which matches at genome position chr20:59993
  • Examine a pileup in text and in IGV

    Code Block
    title Command to generate a "pileup" - data oriented in "genome coordinates" by genome base-pair
    samtools mpileup -f ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | more

    Examine the area around chr20:60614
  • Examine a variant in text and in IGV

    Code Block
    title Command to call variants
    samtools mpileup -uf ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools view -vcg - | more

    - look at the SNP at base 76771
    Examine the SNP at chr20:76771
• SNP Annotation
• Reference databases (if time permits)