Sequencing Data to Databases,BAM Files - IT Assignment Help

Assignment Task

From sequencing data to databases.
A researcher sequenced the genome of people with blond and dark hair using Illumina sequencing.She wants to check whether these people display any known variant that could explain differences in hair colour. To make your analyses faster, only reads mapping near one of the variants of interest are included. There are six individuals in total, sequenced in paired-end (so there are two fastq files per individual). The names of the fastq files are self-explanatory: names starting with “Dark”correspond to people with dark hair; those starting with “Blond” correspond to people with blonde hair. You will align the reads back to the human reference genome and do SNP calling. You need to use the human genome reference called hg38. 
A little help:
The procedure is similar to what we did in the workshops, but you need 1) to assign a unique identifier within each alignment file you produce (adding a Read Group), and 2) to generate a merged BAM file from individual BAM files so you can run the program that calls variants.Otherwise, you will not be able to see the individual genotypes (the SNP caller will assume that all  reads come from a single individual).

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