exome_test.sh is a shell script to run GATK best practice and varscan for variant-calling in exomseq. It uses bwa for alignment, UnifiedGenotyper and varscan to call variants, and Annovar to annotate. It also employs DepthofCoverage and BAM-readcount.

[Notice]
MAF files compatible with MutSigCV are added.
The Annovar filter dbnsfp30a is updated.
Correction of an error in the title line of merge file.
-ni option added.
-vb option (-B in varscan) added
exac03nontcga is added.
An error about VARSCAN is corrected.
Mutlithreading for dbsnp annotation, Haplotypecaller, Varscan and bamreadcount more efficient.
UMI function is added.
Allelic fraction is added.
Better COSMIC and CLINVAR annotation.

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2015-11-15
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