zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #1051 from broadinstitute/ldg_M2_additionalFeatures 

Little changes to M2 code and docs
This commit is contained in:
kcibul 2015-08-28 10:25:23 -04:00
parent 2ac5051767 3dc68732fb
commit 13c5a74cc7
2 changed files with 2 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/variant/GATKVCFConstants.java
View File

@ -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
View File

@ -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"));