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Adding minor clarification to -mbq argument documentation

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Guillermo del Angel 2012-06-05 15:17:56 -04:00
parent 47df7bbc14
commit ce4dc2128d
1 changed files with 1 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -100,6 +100,7 @@ public class UnifiedArgumentCollection {
/** /**
* The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base * The minimum confidence needed in a given base for it to be used in variant calling. Note that the base quality of a base
* is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value. * is capped by the mapping quality so that bases on reads with low mapping quality may get filtered out depending on this value.
* Note too that this argument is ignored in indel calling. In indel calling, low-quality ends of reads are clipped off (with fixed threshold of Q20).
*/ */
@Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false) @Argument(fullName = "min_base_quality_score", shortName = "mbq", doc = "Minimum base quality required to consider a base for calling", required = false)
public int MIN_BASE_QUALTY_SCORE = 17; public int MIN_BASE_QUALTY_SCORE = 17;