search

genome-rcast / karkinos

Tumor genotyper, that detects SNV, absolute CNV and Tumor contents
Apache License 2.0
10 stars 2 forks source link

Loosen the filter condition of INDEL in a normal sample #28

Closed federkasten closed 3 years ago

federkasten commented 3 years ago

This PR adds the threshold for normal INDELs so that the karkinos output them as somatic if INDEL reads exist in a normal sample and it is less than 0.05% AF and less than 2, and if tumor AF is greater than 20 times and more than ten reads in a tumor sample.

Also, this PR includes the following fixes for the features added in #27.

codecov-io commented 3 years ago

Codecov Report

Merging #28 (bb5841e) into feature/softclip-mismatch-filter (873dbd2) will decrease coverage by 0.06%. The diff coverage is 0.00%.

Impacted file tree graph

@@                          Coverage Diff                           @@
##             feature/softclip-mismatch-filter      #28      +/-   ##
======================================================================
- Coverage                               11.18%   11.12%   -0.07%     
  Complexity                                433      433              
======================================================================
  Files                                     134      135       +1     
  Lines                                   12753    12824      +71     
  Branches                                 2257     2283      +26     
======================================================================
  Hits                                     1427     1427              
- Misses                                  11258    11329      +71     
  Partials                                   68       68
Impacted Files Coverage Δ Complexity Δ
.../java/jp/ac/utokyo/rcast/karkinos/exec/PileUP.java 0.00% <0.00%> (ø) 0.00 <0.00> (ø)
.../ac/utokyo/rcast/karkinos/exec/TumorGenotyper.java 0.00% <0.00%> (ø) 0.00 <0.00> (ø)
...utokyo/rcast/karkinos/filter/FilterAnnotation.java 0.00% <0.00%> (ø) 0.00 <0.00> (ø)
...tokyo/rcast/karkinos/filter/SupportReadsCheck.java 0.00% <0.00%> (ø) 0.00 <0.00> (ø)
...utokyo/rcast/karkinos/filter/TerminalMismatch.java 0.00% <0.00%> (ø) 0.00 <0.00> (ø)
.../jp/ac/utokyo/rcast/karkinos/utils/DataHolder.java 0.00% <ø> (ø) 0.00 <0.00> (ø)
...jp/ac/utokyo/rcast/karkinos/utils/GeneEachCNV.java 0.00% <ø> (ø) 0.00 <0.00> (ø)
...va/jp/ac/utokyo/rcast/karkinos/utils/SamUtils.java 0.00% <0.00%> (ø) 0.00 <0.00> (?)

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 873dbd2...bb5841e. Read the comment docs.

federkasten commented 3 years ago

@alumi @xckitahara I have completed the verification. I would appreciate it if you review it. :pray:

federkasten commented 3 years ago

@alumi @xckitahara Thanks for your review! :pray: