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Go to this web page and call variants from real human genomes from the 1000 genomes project. |
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).
Examine the first read of the file which matches at genome position chr20:59993Code 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 a pileup in text and in IGV
Examine the area around chr20:60614Code 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 a variant in text and in IGV
- look at the SNP at base 76771Code Block title Command to call variants samtools mpileup -uf ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools view -vcg - | more
Examine the SNP at chr20:76771
- Examine a pileup in text and in IGV
- SNP Annotation
- Reference databases (if time permits)