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Little changes to M2 code and docs 

Make MQ threshold a parameter (compare to M1 by setting to zero)
Add logic for multiple alternate alleles in tumor
Exclude MQ0 normal reads from normal LOD calculation
Fix path errors in Dream_Evaluations.md
Move M2 eval scripts out of walkers package so they run
This commit is contained in:
Laura Gauthier 2015-04-24 11:03:00 -04:00
parent 2ac5051767
commit 3dc68732fb
2 changed files with 2 additions and 0 deletions
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1
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
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@ -144,6 +144,7 @@ public final class GATKVCFConstants {
public static final String PON_FILTER_NAME = "panel_of_normals"; //M2
public static final String STR_CONTRACTION_FILTER_NAME = "str_contraction"; //M2
public static final String TUMOR_LOD_FILTER_NAME = "t_lod_fstar"; //M2
public static final String TRIALLELIC_SITE_FILTER_NAME = "triallelic_site"; //M2
// Symbolic alleles
public final static String SYMBOLIC_ALLELE_DEFINITION_HEADER_TAG = "ALT";

1
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFHeaderLines.java
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@ -70,6 +70,7 @@ public class GATKVCFHeaderLines {
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.PON_FILTER_NAME, "Seen in at least 2 samples in the panel of normals"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.TUMOR_LOD_FILTER_NAME, "Tumor does not meet likelihood threshold"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.STR_CONTRACTION_FILTER_NAME, "Site filtered due to contraction of short tandem repeat region"));
addFilterLine(new VCFFilterHeaderLine(GATKVCFConstants.TRIALLELIC_SITE_FILTER_NAME, "Site filtered because more than two alt alleles pass tumor LOD"));
addFormatLine(new VCFFormatHeaderLine(ALLELE_BALANCE_KEY, 1, VCFHeaderLineType.Float, "Allele balance for each het genotype"));
addFormatLine(new VCFFormatHeaderLine(MAPPING_QUALITY_ZERO_BY_SAMPLE_KEY, 1, VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample"));