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P000001193

GATK-UnifiedGenotyper-snpEff (hs37d5 only) [IN: bam (max 10)]


Introduction


Call genomic variants with GATK; thereafter add annotation including prediction with snpEff. This is for human hg19(hs37d5) use only.


Input formatBAM
Library layoutUnspecified
SpeciesHuman(hs37d5) only
Execution timeAbout 2 hours (9M paired-end reads[76bp+76bp])



Results
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Workflow
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Inputs


Multiple sorted alignment files in BAM format with the index files.
SAM/BAM Format Specification(external link)

Outputs


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Options


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Use case







Public
SAMtools(Original site)(external link)(NGS Surfer's wiki)(external link)
GATK(Original site)(external link)
snpEff(Original site)(external link)(NGS Surfer's wiki)(external link)