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=Genotyping= [[Daniel:Notebook/Haplotyping|Back to Notebook]] This page focuses on my work regarding genotyping the different data sets from the haplotyping project. Genotyping is, in a sense, the first step in haplotyping, because you need to be able to identify heterozygous SNPs. Most programs, like HAPCUT, require a vcf that already states the locations of the heterozygous SNPs before running. ==Analyzing Genotyping Abilities of Different Data Sets== In the final step, I use the following [[File:ROC.freebayes.zip|MATLAB code]] to create the ROC curve. You can view the [[Media:Freebayes_roc_master.txt|master file]] as media on the wiki. The steps are: #Read in the infofile, which is a file that lists all the files you'd like to use for the analysis. The files may also have a tag, which is used for labeling. One file must be labeled "true" in order to analyze everything against a true VCF #Next loads in position data for true file, and position and quality data for the test data #Compares true positions against test positions, overlaps with the true data are considered "true" and all others are "false" #False discovery rate and sensitivity are calculated using the "false" and "true" data sets, respectively. ==Individual Data Sets== ===BAC=== BAC was able to be analyzed by freebayes using its standard bam files. Since each bam was sorted by index, not chromosome, I used every bam file, extracting each chromosome for analysis individually. [[Media:Bac.freebayes.sh|script]] ===Hi-C=== Hi-C was able to be analyzed by freebayes using its standard bam files. Since each bam was sorted by chromosome, I simply looped through each. [[Media:Freebayes.sh|script]]
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