justinjj24
commented
8 years ago Hi Andreas, Yes I'm also not sure what to use here as standard and i see this value in forum and asif strongly suggest from best practices for mutect using lod 0.4 and will find and send the reference.
-LOD 0.4 (5.0 default). (This term is equivalent to "significance" - i.e. is the improvement significant enough to merit realignment? Note that this number should be adjusted based on your particular data set. For low coverage and/or when looking for indels with low allele frequency, this number should be smaller.) Thanks Justin
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-------- Original message -------- From: Andreas Wilm notifications@github.com Date: 26/08/2016 08:55 (GMT+05:30) To: gis-rpd/pipelines pipelines@noreply.github.com Cc: Justin Jeyakani gnanakkan@gis.a-star.edu.sg, Assign assign@noreply.github.com Subject: [gis-rpd/pipelines] Reference for LOD 0.4 in IndelRealigner for Mutect (#73)
Hello, I couldn't a reference that suggested to use LOD 0.4 for IndelRealigner for Mutect as suggested by your writeup. Would you still have that? Thanks
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andreas-wilm
Hello, I couldn't a reference that suggested to use LOD 0.4 for IndelRealigner for Mutect as suggested by your writeup. Would you still have that? Thanks