Compare GATK's internal pileup to a reference Samtools pileup
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
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--pileup | NA | Pileup generated by Samtools | |
Optional Outputs | |||
--out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
Optional Flags | |||
--continue_after_error | false | Continue after encountering an error |