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We would normally use the BAM file from the previous mapping step to call variants in this raw data. However, for the purposes of this course we will use the actual BAM file provided by the 1000 Genomes Project (from which the .fastq file above was derived, leading to some oddities in it).
$SCRATCH/BDIB_Human_tutorial/raw_files/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam
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