Assignment Analysis

Minimum one paragraph each.

How did samples differ from each other in read count versus in read quality? Why does each matter for SNP calling?

Sample B had low coverage, approximately 1/4 of the coverage that the rest of the samples had. Low coverage leads to a lower reading depth, which can lead to misinterpretation of heterozygous loci and variant alleles, causing FN and FP. It can also causes gaps in the genomic region coverage (Sample B had 98.1% genome coverage while the rest of the samples yielded 100%). Sample D had low quality, which a mean phred score of 20, while the other samples had phred scores around 35. This can cause misaignment and issues with calling like FN and FP. Sample C had a poly-G tail, which just needed to be trimmed, and Sample A had no issues.

What are the relative merits and drawbacks of filtering? Interpret the above chart in terms of the original quality issues, and how those yielded different outcomes. When is filtering a good idea vs when it is it a bad idea? Think specifically about false positives vs false negatives.

Pick two false negatives and two false positives, from any sample. For each, tell me the sample, tell me the chromosome and coordinate location, put in a screenshot of IGV or JBrowse, and explain the specific cause of the FN or FP call.