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Converting ModelSegments outputs for ABSOLUTE
Lea_F
Member ❠
I work on exome data to detect somatic variants. I identified the SNPs/Indels with Mutect2 and I followed the ModelSegments tutorial to detect CNAs. Now I want to convert the AF outputs I got with ModelSegments into AllelicCapSeg outputs to use them with ABSOLUTE.
For this purpose, I tried to use part of this pipeline on GitHub (unsupported/combine_tracks_postprocessing_cnv/combine_tracks.wdl) to convert the data with the function "convert_model_segments_to_alleliccapseg". I use as input the.af.param and.cr.seg files from ModelSegments.
However, I don't really understand in the script the utility of the following parameters to use as threshold values (Float ? maf90_threshold and Int ? min_hets_acs_results)?
Is there a better way to do this conversion?
Thank you
Best Answer
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LeeTL1220
Arlington, MA ✭✭✭
@Lea_F Hello, this WDL is unsupported, because we have little evaluation data and we are going to do a different approach in the long-term ...
but for now ....
Are you using the blacklisted intervals when running ModelSegments? If so, try setting the maf90 threshold to 0.485. If not, use the blacklists as input to ModelSegments. The somatic CNV WDL (that runs ModelSegments) has some reasonable, public files in the preamble.
If your data is WGS, set the min_hets_acs_results to 10, otherwise, 2 is reasonable.
These suggestions are not based on a lot of evaluations, but should help your ModelSegments results.
To the best of my knowledge, there is no better conversion. User feedback thusfar has indicated that this conversion process produces the best ABSOLUTE results, even if it is heavy on heuristics.
Answers
Hi @Lea_F ,
This is one of the few workflows in the GATK repo we do not support. We can help you with questions on workflows outside of the "unsupported" directory.
@Lea_F Hello, this WDL is unsupported, because we have little evaluation data and we are going to do a different approach in the long-term ...
but for now ....
Are you using the blacklisted intervals when running ModelSegments? If so, try setting the maf90 threshold to 0.485. If not, use the blacklists as input to ModelSegments. The somatic CNV WDL (that runs ModelSegments) has some reasonable, public files in the preamble.
If your data is WGS, set the min_hets_acs_results to 10, otherwise, 2 is reasonable.
These suggestions are not based on a lot of evaluations, but should help your ModelSegments results.
To the best of my knowledge, there is no better conversion. User feedback thusfar has indicated that this conversion process produces the best ABSOLUTE results, even if it is heavy on heuristics.