https://github.com/mskcc/vcf_accuracy

vcf accuracy evaluator using VT, BEDTOOLS, PyVCF, and TABIX
https://github.com/mskcc/vcf_accuracy

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vcf accuracy evaluator using VT, BEDTOOLS, PyVCF, and TABIX

• Host: GitHub
• URL: https://github.com/mskcc/vcf_accuracy
• Owner: mskcc
• Created: 2015-08-12T15:15:00.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2016-05-24T15:28:24.000Z (over 8 years ago)
• Last Synced: 2023-08-06T05:35:24.592Z (over 1 year ago)
• Language: Python
• Size: 1000 KB
• Stars: 1
• Watchers: 80
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
![VCFs are Great](http://i.imgur.com/E8gfNu0.gif "Aww Yeah Accuracy Time!")

Install some Libs

=================

* use THIS python for below commands, so we get argparse + all these libs:

* /opt/common/CentOS_6-dev/python/python-2.7.10/bin/python

* download/install cmo package 

* git clone https://github.com/mskcc/cmo.git

* python setup.py install --user

* download/install magic package

* https://pypi.python.org/packages/source/f/filemagic/filemagic-1.6.tar.gz

* tar -xvf and python setup.py install --user

* download/install pyvcf

* https://pypi.python.org/packages/source/P/PyVCF/PyVCF-0.6.7.tar.gz

* tar -xvf and python setup.py install --user

Expected formatting

===================

MAF input requirements

----------------------

* Requires standard TCGA MAF columns (https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification):

  * Hugo_Symbol, Entrez_Gene_ID, Center, NCBI_Build, Chromosome, Start_Position, End_Position,

    Strand, Variant_Classification, Variant_Type, Reference_Allele, Tumor_Seq_Allele1, Tumor_Seq_Allele2,

    dbSNP_RS, dbSNP_Val_Status, Tumor_Sample_Barcode, Matched_Norm_Sample_Barcode, Match_Norm_Seq_Allele1,

    Match_Norm_Seq_Allele2, Tumor_Validation_Allele1, Tumor_Validation_Allele2, Match_Norm_Validation_Allele1,

    Match_Norm_Validation_Allele2, Verification_Status, Validation_Status, Mutation_Status, Sequencing_Phase,

    Sequence_Source, Validation_Method, Score, BAM_File, Sequencer

* Requires MSKCC specific columns:

  * n_ref_count, n_alt_count, n_depth, t_alt_count, t_ref_count, t_depth

* If subsetting the bedfile chromosome labelling must match the variant file style chr1 vs. 1, MT vs. M etc.

* Pre-normalized datasets must be left aligned and processed using VT (http://genome.sph.umich.edu/wiki/Vt).