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Update outdated links to HaplotypeMap file format #1988

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Jan 13, 2025
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Original file line number Diff line number Diff line change
Expand Up @@ -99,7 +99,7 @@ public class CalculateFingerprintMetrics extends CommandLineProgram {
public File OUTPUT;

@Argument(shortName = "H", doc = "The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See " +
"https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
"https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for details.")
public File HAPLOTYPE_MAP;

@Argument(doc = "Specificies which data-type should be used as the basic unit. Fingerprints from readgroups can " +
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2 changes: 1 addition & 1 deletion src/main/java/picard/fingerprint/CheckFingerprint.java
Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,7 @@ public class CheckFingerprint extends CommandLineProgram {
public String EXPECTED_SAMPLE_ALIAS;

@Argument(shortName = "H", doc = "The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See " +
"https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
"https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for details.")
public File HAPLOTYPE_MAP;

@Argument(shortName = "LOD", doc = "When counting haplotypes checked and matching, count only haplotypes " +
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Original file line number Diff line number Diff line change
Expand Up @@ -353,7 +353,7 @@ public class CrosscheckFingerprints extends CommandLineProgram {
public File MATRIX_OUTPUT = null;

@Argument(shortName = "H", doc = "The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See " +
"https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
"https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for details.")
public File HAPLOTYPE_MAP;

@Argument(shortName = "LOD",
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2 changes: 1 addition & 1 deletion src/main/java/picard/fingerprint/ExtractFingerprint.java
Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ public class ExtractFingerprint extends CommandLineProgram {
public File OUTPUT;

@Argument(shortName = "H", doc = "A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See " +
"https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
"https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for details.")
public File HAPLOTYPE_MAP;

@Argument(shortName = "C", doc = "A value of estimated contamination in the input. A non-zero value will cause the program to provide a better estimate of the fingerprint in the presence of contaminating reads",
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2 changes: 1 addition & 1 deletion src/main/java/picard/fingerprint/IdentifyContaminant.java
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ public class IdentifyContaminant extends CommandLineProgram {
public File OUTPUT;

@Argument(shortName = "H", doc = "A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. See " +
"https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details.")
"https://gatk.broadinstitute.org/hc/en-us/articles/360035531672-Haplotype-map-format for details.")
public File HAPLOTYPE_MAP;

@Argument(shortName = "C", doc = "A value of estimated contamination in the input. ", minValue = 0D, maxValue = 1D)
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