Fixing csv_to_maf to take care of IMPACT normals

0.1.5

Fixing csv_to_maf to take care of IMPACT normals

Wrapper for create_report.R

1. Running create_report.R on multiple samples with ability to select best fit

Patch Release to read DMP Key file

• Fix the way DMP KEY file is read

Update on get_cbioportal_variants.py

Adding modification to get_cbioportal_variants.py to handle subsetting:

• sv,
• cna,
• clinical patient, and
• clinical sample files

Incorporating Clinical ACCESS to genotype all.

• Adding compile_reads_all.R for genotyping Clinical MSK-ACCESS along with Clinical MSK-IMPACT and Research ACCESS

Bug Fix

#66

Utility scripts and improvements

✔️ Script to find dmp mutations and tag them covered or not based on bed file
✔️ Script to convert dates to days based on the baseline sample date
✔️ Changing default folder for SV incorporation script for dmp
✔️ In create_report.R adding option to make plots without the separation based on clonality (thank you @murphycj2 )
✔️ In create_report.R adding an option to plot impact VAF as well (thank you @murphycj2 )

Bug Fix

• Allowing more colors for the annotation track
• The updating default path to clinical data in CNA script
• Giving default path to writing clonal mutation files

Bug fix for OR symbol in compile_read.R

Merge pull request #56 from msk-access/develop

Bug fix for OR sign

Add DMP normals to genotyping

Merge pull request #54 from msk-access/develop

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