Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T CheckPileup -R reference.fasta -I your_data.bam --pileup:SAMPileup pileup_file.txt -L chr1:257-275 -o output_file_name


Manual

Argument name(s)Default valueSummary
Required Inputs
--pileup
NAPileup generated by Samtools
Optional Outputs
--out
 -o
stdoutAn output file created by the walker. Will overwrite contents if file exists
Optional Flags
--continue_after_error
falseContinue after encountering an error


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