Answers and explanations for exercises of intro lesson 00

[naurasd]

Hi

thanks for putting together these great learning resources.

Would it be possible to add the correct answers and some explanations to the exercises at the end of intro lesson 00?

Thank you! Nauras

[Gammerdinger]

Thanks for the kind words Nauras! We can develop an answer key, but this exercise was more rhetorical in nature as we wanted to hopefully demonstrate how tricky this task can be for variant calling algorithms. In the meantime, we have drafted a rough draft of our thoughts on how we think we would answer the questions. I will assign this to myself and draft up a more formal answer key that will come in a few months when we review the materials prior to the next variant calling workshop. We hope this is acceptable!

1. More likely to be a somatic variant because there isn't closer to a 50:50 distribution of reference and alternate alleles. However, it can be difficult to draw conclusions from such low sequencing depth.
2. Not very confident, maybe it is a sequencing error, but in general for most heterozygous germline mutations we would expect to get more "T" alleles from our sequencing
3. Still not very confident as we only have 2 reads of support but it feels like this is more in-line with expectations for a somatic mutation rather than germline
4. Not particularly confident with such a low sequencing depth
5. More sequencing depth

Best, Will Gammerdinger

[naurasd]

Hi Will

thanks for the taking the time to draft the answers and for replying so quick.

I understand that the questions were of rhetorical nature, but students like me really appreciate to get some more information if exercises like these are posted with the learning material.

thanks for the answers, they do help me to better understand the topic.

best, Nauras