GotCloud: Variant Calling Pipeline

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The Variant Calling Pipeline (UMAKE) takes recalibrated BAM files and detects SNPs and calls their genotypes, producing VCF files.

Input Data:

  • Aligned/Processed/Recalibrated BAM files
  • Index file containing Sample IDs & BAM file names
  • Reference files
  • (Optional) Configuration file to override default options

BAM files

Index file

Reference Files

Configuration File

Running

Running umake is straightforward: 

cd ~/myseq
/usr/local/biopipe/bin/umake --conf myconf ???
make -f [out-prefix].Makefile -j [# parallel jobs]

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