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Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
Matt Hanna 2011-09-26 15:12:52 -04:00
parent 059cdcb1be 317b95fa57
commit 6478681c0c
2 changed files with 17 additions and 6 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
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@ -19,8 +19,19 @@ import java.util.Map;
/**
* Total (unfiltered) depth over all samples.
*
* Affected by downsampling (-dcov) though, so the max value one can obtain for N samples with -dcov D
* is N * D
* This and AD are complementary fields that are two important ways of thinking about the depth of the data for this sample
* at this site. The DP field describe the total depth of reads that passed the Unified Genotypers internal
* quality control metrics (like MAPQ > 17, for example), whatever base was present in the read at this site.
* The AD values (one for each of REF and ALT fields) is the count of all reads that carried with them the
* REF and ALT alleles. The reason for this distinction is that the DP is in some sense reflective of the
* power I have to determine the genotype of the sample at this site, while the AD tells me how many times
* I saw each of the REF and ALT alleles in the reads, free of any bias potentially introduced by filtering
* the reads. If, for example, I believe there really is a an A/T polymorphism at a site, then I would like
* to know the counts of A and T bases in this sample, even for reads with poor mapping quality that would
* normally be excluded from the statistical calculations going into GQ and QUAL.
*
* Note that the DP is affected by downsampling (-dcov) though, so the max value one can obtain for N samples with
* -dcov D is N * D
*/
public class DepthOfCoverage extends InfoFieldAnnotation implements StandardAnnotation {

8
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -24,9 +24,9 @@ import java.util.Map;
/**
* The depth of coverage of each VCF allele in this sample
* The depth of coverage of each VCF allele in this sample.
*
* Complementary fields that two important ways of thinking about the depth of the data for this sample
* This and DP are complementary fields that are two important ways of thinking about the depth of the data for this sample
* at this site. The DP field describe the total depth of reads that passed the Unified Genotypers internal
* quality control metrics (like MAPQ > 17, for example), whatever base was present in the read at this site.
* The AD values (one for each of REF and ALT fields) is the count of all reads that carried with them the
@ -38,8 +38,8 @@ import java.util.Map;
* normally be excluded from the statistical calculations going into GQ and QUAL. Please note, however, that
* the AD isn't necessarily calculated exactly for indels (it counts as non-reference only those indels that
* are actually present and correctly left-aligned in the alignments themselves). Because of this fact and
* because the AD includes reads and bases that were filtered by the Unified Genotyper, one should not base
* assumptions about the underlying genotype based on it; instead, the genotype likelihoods (PLs) are what
* because the AD includes reads and bases that were filtered by the Unified Genotyper, <b>one should not base
* assumptions about the underlying genotype based on it</b>; instead, the genotype likelihoods (PLs) are what
* determine the genotype calls (see below).
*/
public class DepthPerAlleleBySample extends GenotypeAnnotation implements StandardAnnotation {