ISmolicz
- Total activity 188
- Last activity
- Member since
- Following 0 users
- Followed by 0 users
- Votes 11
- Subscriptions 100
Activity overview
Latest activity by ISmolicz-
ISmolicz commented,
Thank you for your reply David Benjamin. Apologies, I did not realise it was still an existing argument as it was not listed in the Mutect2 documentation argument list. My colleague ran the command...
-
ISmolicz created a post,
What argument(s) should be used instead of --debug-graph-transformations?
Hello GATK Team, The documentation entitled 'When HaplotypeCaller and Mutect2 do not call an expected variant' suggests running Mutect2 with the argument --debug-graph-transformations set as true a...
-
ISmolicz commented,
Thank you for your reply David Benjamin. To clarify my above question, are there any other arguments in this troubleshooting document that should be set to true from the outset when using Mutect2 n...
-
ISmolicz commented,
Hi David Benjamin, Thank you for your reply. The functions of the arguments --genotype-germline-sites and --genotype-pon-sites are described with similar terminology in the Mutect2 documentation. H...
-
ISmolicz commented,
Hi David Benjamin, Thank you for answering my queries. Would it be possible to expand on the answer to Q3 above a little further: 1. How does trimming lead to having a Linked De Bruijn graph as you...
-
ISmolicz commented,
Hi David Benjamin, Thank you for your reply and for the advice that --linked-de-bruijn-graph should be the default now. Just to mention in case this is helpful, Mutect2 documentation advises that t...
-
ISmolicz commented,
Hi David Benjamin, Thank you for your reply to my post above. Please may I ask why using the --linked-de-bruijn-graph is not an argument that is set to true by default and is only recommended when ...
-
ISmolicz commented,
Hi David Benjamin, Thank you for your reply to my post. By changing the arguments --genotype-germline-sites and --genotype-pon-sites to true, what does this change in the Mutect2 output? Would vari...
-
ISmolicz commented,
Hi Nicolas Loucheu, Thank you for your reply to my post. I do not have an update yet, but will post if I do. Kind regards.
-
ISmolicz commented,
Hi David Benjamin, Following your post above, if a variant was in the germline resource and/or the panel of normals, would it still not be output by Mutect2 and then labelled with 'germline' and/or...