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We'll return to this example data shortly to demonstrate a much more involved tool, GATK, to do the same steps.
Note if you're trying this on Stampede: The $BI directory is not accessible from compute nodes on Stampede so you will need to make a copy of your data on $SCRATCH and update file locations accordingly to get this demo to run.
Optional: Mapping Exercise
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samtools mpileup -uf $BI/ref_genome/fasta/ucsc/ucsc.hg19.fasta \ $BI/ngs_course/human_variation/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam \ | bcftools view -vcg - > test.raw.bcfvcf |
Note that the reference chosen for mpileup must be exactly the same as the reference used to create the bam file. The 1000 genomes project has created it's own reference and so the command listed above won't work - we have to use the 1000 genomes reference which is $BI/ngs_course/human_variation/ref/hs37d5.fa. We could have chosen another mapper if we'd wanted to though.
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