VcfCooker

vcfCooker is a software that converts VCF/BED file formats in various forms. vcfCooker is currently under development, and will be publicly released soon. The current documentation contains the minimal information of currently working functions.

Current Binary Location

Current binary version of vcfCooker is available at /net/fantasia/home/hmkang/sw/vcfCooker .

Basic Usage

The following parameters are available.  Ones with "[]" are in effect:

Available Options
                         Recipes : --write-bed, --write-vcf, --upgrade,
                                   --summarize, --filter, --subset
               VCF Input options : --in-vcf []
               BED Input options : --in-bfile [], --in-bed [], --in-bim [],
                                   --in-fam [],
                                   --ref [/data/local/ref/karma.ref/human.g1k.v37.fa]
              Subsetting options : --in-subset [], --mono-subset,
                                   --filt-only-subset
                  Output Options : --out [./vcfCooker], --qGeno,
                                   --print-every [10000]
      Output compression Options : --plain [ON], --bgzf, --gzip
   Genotype-level Filter Options : --minGQ, --minGD
                  Filter Options : --winIndel, --indelVCF [], --minQUAL,
                                   --minMQ, --maxDP [2147483647], --minDP,
                                   --maxABL [100], --winFFRQ, --maxFFRQ,
                                   --winFVAR, --merFVAR, --maxFVAR, --minNS,
                                   --maxSTP [2147483647],
                                   --maxTTT [2147483647],
                                   --minTTT [-2147483648], --maxSTR [100],
                                   --minSTR [-100], --maxSTZ [2147483647],
                                   --minSTZ [-2147483648], --maxCBR [100],
                                   --minCBR [-100], --maxQBR [100],
                                   --minQBR [-100], --maxCBZ [2147483647],
                                   --maxCSR [100], --minCSR [-100],
                                   --maxLQZ [2147483647],
                                   --minLQZ [-2147483648],
                                   --maxRBZ [2147483647],
                                   --minRBZ [-2147483648],
                                   --maxIOZ [2147483647],
                                   --minIOR [-2147483648],
                                   --maxIOR [2147483647],
                                   --maxAOZ [2147483647],
                                   --maxAOI [2147483647], --maxMQ0 [100],
                                   --maxMQ10 [100], --maxMQ20 [100],
                                   --minFIC [-2147483648], --minABE [-100],
                                   --maxABE [100], --maxLQR [100],
                                   --minMBR [-100], --maxMBR [100],
                                   --minABZ [-2147483648],
                                   --maxABZ [2147483647],
                                   --maxBCS [2147483647], --keepFilter

Upgrading glfMultiples outputs (v 3.3 to v 4.0)

If you have a output from glfMultiples (06-16-2010), you can upgrade the output files using the following command

vcfCooker --in-vcf [input-vcf-file-from-glfMultiples] --upgrade --out [output-vcf-file]

Upgraded VCFs will have the following improvements.

• The additional tab between FORMAT field and genotype values will be removed, if exists
• The REF and ALT alleles will be presented as capital letters.
• The FORMAT field value, GT:GD:GQ will be changed to GT:DP:GQ:PL
• depth will be changed to DP in the INFO field
• mapQ will be changed to MQ in the INFO field
• MAF will be changed to AF (AlleleFrequency) in the INFO field, with proper changes if needed.
• NS (NumSamples) will be added as a new INFO field
• AC (AlleleCount) will be added as a new INFO field
• AN (NumAlleles) will be added as a new INFO field
• AB (AlleleBalance) will be added as a new INFO field (suggested by Tom Blackwell at Genotype_Likelihood_Based_Allele_Balance)

Filtering a VCF file

A example command line of upgrading / filtering a glfMultiples output is as follows.

vcfCooker --in-vcf /home/csidore/1000g_CEUTSI_WG/analysis_chr20/vcf/TSI+CEU+GBR.Q10.chr20.vcf --out 1KG.20100517.EUR.chr20.vcf.gz --bgzf --upgrade \
 --filter --maxAB 65 --indelVCF /share/swg/hmkang/data/1000G/pilot_indels_2010_07/1kg.pilot_release.merged.indels.sites.hg19.chr20.vcf --winIndel 10 \
 --minDP 93 --maxDP 1860 --minNS 19 --minQUAL 10 --write-vcf --winFFRQ 10 --maxFFRQ 30

Acknowledgements

vcfCooker is a result from collaborative effort by Hyun Min Kang, Matthew Flickinger, Matthew Snyder, Paul Anderson, Tom Blackwell, Mary Kate Trost, and Goncalo Abecasis. Please email to Hyun Min Kang [hmkang@umich.edu ] for any questions.