VarScan

Reference

Reports the read counts for each base at positions in a pileup file

Category

Variant Analysis

Usage

java -jar VarScan.jar readcounts [pileup file] OPTIONS

Manual

--variants-file A list of variants at which to report readcounts
--output-file   Output file to contain the readcounts
--min-coverage  Minimum read depth at a position to make a call [8]
--min-base-qual Minimum base quality at a position to count a read [30]

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