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steverozen / ICAMS

ICAMS: In-depth Characterization and Analysis of Mutational Signatures
GNU General Public License v3.0
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Question: possible to get context/category sssignment of each mutation in VCF? #3

Closed ahwanpandey closed 4 years ago

ahwanpandey commented 4 years ago

Good morning,

I was wondering if there was a way to get the assignment of each mutation in the VCF to the signature context? Foe example for a few lines of the VCF as follows:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  SampleID
1   60868313    .   AAG A   .   PASS    .   GT:AD:AF:DP 0/1:58,22:0.275:80
1   110005445   .   CAA C   .   PASS    .   GT:AD:AF:DP 0/1:24,19:0.442:55
1   235268805   .   TAA T   .   PASS    .   GT:AD:AF:DP 0/1:39,35:0.473:116
2   22105991    .   CAT C   .   PASS    .   GT:AD:AF:DP 0/1:10,13:0.565:27

Could ICAMs return something that contains the context assigned for each mutation such that it could be concatenated to a table? eg..

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  SampleID    ICAMS_context
1   60868313    .   AAG A   .   PASS    .   GT:AD:AF:DP 0/1:58,22:0.275:80    DEL:repeats:2:5+
1   110005445   .   CAA C   .   PASS    .   GT:AD:AF:DP 0/1:24,19:0.442:55    DEL:repeats:2:5+
1   235268805   .   TAA T   .   PASS    .   GT:AD:AF:DP 0/1:39,35:0.473:116    DEL:repeats:2:5+
2   22105991    .   CAT C   .   PASS    .   GT:AD:AF:DP 0/1:10,13:0.565:27    DEL:repeats:2:5+

This would be really helpful to an already awesome package.

Thanks, Ahwan

jnh01 commented 4 years ago

@ahwanpandey Thanks a lot for your suggestion. We have updated functions MutectVCFFilesToCatalog, MutectVCFFilesToCatalogAndPlotToPdf and MutectVCFFilesToZipFile such that object catID from the returned list has been changed from an ID catalog to a list: the second element annotated.vcfs is a list of data frames which contain the original VCF ID mutation rows with three additional columns seq.context.width, seq.context and ID.class added. You can get category assignment of each ID mutation in VCF from ID.class column.

The returned value from functions StrelkaIDVCFFilesToCatalog, StrelkaIDVCFFilesToCatalogAndPlotToPdf, StrelkaIDVCFFilesToZipFile and VCFsToIDCatalogs also contain the ID category assignment information. You may refer to the updated reference manual with link provided on README.md for more details.

Please install the latest ICAMS development version 2.1.2.9005 from GitHub master branch with installation methods listed on README.md.

If you have other suggestion about this package or find any bug, please let us know. Thanks!

ahwanpandey commented 4 years ago

Thanks @jnh01 for the prompt response and the solution!