diff --git a/src/main/java/picard/fingerprint/CalculateFingerprintMetrics.java b/src/main/java/picard/fingerprint/CalculateFingerprintMetrics.java index 1ea18b52e8..4f315f7606 100644 --- a/src/main/java/picard/fingerprint/CalculateFingerprintMetrics.java +++ b/src/main/java/picard/fingerprint/CalculateFingerprintMetrics.java @@ -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 " + diff --git a/src/main/java/picard/fingerprint/CheckFingerprint.java b/src/main/java/picard/fingerprint/CheckFingerprint.java index e35843f6fe..2baa4fb475 100644 --- a/src/main/java/picard/fingerprint/CheckFingerprint.java +++ b/src/main/java/picard/fingerprint/CheckFingerprint.java @@ -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 " + diff --git a/src/main/java/picard/fingerprint/CrosscheckFingerprints.java b/src/main/java/picard/fingerprint/CrosscheckFingerprints.java index eb2b53f0fe..bbf2dece45 100644 --- a/src/main/java/picard/fingerprint/CrosscheckFingerprints.java +++ b/src/main/java/picard/fingerprint/CrosscheckFingerprints.java @@ -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", diff --git a/src/main/java/picard/fingerprint/ExtractFingerprint.java b/src/main/java/picard/fingerprint/ExtractFingerprint.java index 5b4e8b8e68..3dfc4ef2a7 100644 --- a/src/main/java/picard/fingerprint/ExtractFingerprint.java +++ b/src/main/java/picard/fingerprint/ExtractFingerprint.java @@ -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", diff --git a/src/main/java/picard/fingerprint/IdentifyContaminant.java b/src/main/java/picard/fingerprint/IdentifyContaminant.java index 94c7365bb7..27b01baa14 100644 --- a/src/main/java/picard/fingerprint/IdentifyContaminant.java +++ b/src/main/java/picard/fingerprint/IdentifyContaminant.java @@ -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)