unifiedgenotyper

Discussion List

• Multisample SNP Calling

  Accepted Answer 656 views 7 comments 0 points Most recent by bhanuGandham May 3Ask the GATK team
• Regarding different genotype calls for same sample using Unified Genotyper & Haplotype Caller

  Answered 15 views 1 comment 0 points Most recent by bhanuGandham April 29Ask the GATK team
• Difference between HC and UG methods

  Answered 23 views 1 comment 0 points Most recent by bhanuGandham March 28Ask the GATK team
• How to find HaplotypeScore?

  Answered 23 views 1 comment 0 points Most recent by SkyWarrior February 28Ask the GATK team
• Coverage bias in HaplotypeCaller

  Answered 804 views 7 comments 0 points Most recent by MehulS January 19Ask the GATK team
• Should I use UnifiedGenotyper or HaplotypeCaller to call variants on my data?

  10K views 8 comments 0 points Most recent by MehulS December 2018Frequently Asked Questions
• Can I use GATK on non-diploid organisms?

  8.7K views 26 comments 1 point Most recent by RSmithAg November 2018Frequently Asked Questions
• I expect to see a variant at a specific site, but it's not getting called

  7.9K views 41 comments 0 points Most recent by luciaUY November 2018Solutions to Problems
• Meaning of --min_base_quality_score

  153 views 8 comments 0 points Most recent by tytolin October 2018Ask the GATK team
• Variant calling: Bam file is indexed but GATK thinks it is not

  Answered 56 views 1 comment 0 points Most recent by bhanuGandham October 2018Ask the GATK team
• Recommended/required sequencing depth for standard diploid, whole-genome, germline variant calling

  Accepted Answer 432 views 15 comments 0 points Most recent by bhanuGandham September 2018Ask the GATK team
• Is UnifiedGenotyper actually better than HaplotypeCaller for this pooled sample project?

  Answered 280 views 2 comments 0 points Most recent by annaship July 2018Ask the GATK team
• UnifiedGenotyper error: Somehow the requested coordinate is not covered by the read.

  Answered 4.6K views 77 comments 0 points Most recent by macko.tipor June 2018Ask the GATK team
• How to run GATK directly on SRA files

  Accepted Answer 1.3K views 12 comments 0 points Most recent by Sheila May 2018Ask the GATK team
• How to set parameter in UnifiedGenotype mode like samtools mpileup

  Accepted Answer 75 views 6 comments 0 points Most recent by Sheila April 2018Ask the GATK team
• Calling variants on whole exome and whole genome samples together?

  Accepted Answer 1.1K views 10 comments 1 point Most recent by Samir March 2018Ask the GATK team
• Consistent 503 Error For engine functions

  Answered 40 views 1 comment 0 points Most recent by ChrisL December 2017Ask the Cromwell + WDL Team
• X Chromosome gentyping

  Accepted Answer 3.2K views 22 comments 0 points Most recent by garrulus_glandarius November 2017Ask the GATK team
• In haplotype variant caller for the Influenza virus, do I need to mention or remove any parameters?

  Answered 182 views 3 comments 0 points Most recent by shlee November 2017Ask the GATK team
• UnifiedGenotyper takes too long to init with big reference

  Accepted Answer 101 views 4 comments 0 points Most recent by Sheila November 2017Ask the GATK team
• How to make results from GAT4.beta.3 "HaplotypeCaller" comparable to GATK2.7's "UnifiedGenotyper"?

  Answered 95 views 2 comments 0 points Most recent by Geraldine_VdAuwera August 2017Ask the GATK team
• Does HaplotypeCaller detect SNPs which are heterozygous (not matching the refrence allele)?

  Answered 74 views 2 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• UnifiedGenotyper miss some alleles while using GENOTYPE_GIVEN_ALLELES mode

  173 views 6 comments 0 points Most recent by Sheila August 2017Ask the GATK team
• SnpEff html and .vcf file result are not matching

  Answered 98 views 1 comment 0 points Most recent by Geraldine_VdAuwera August 2017Ask the GATK team
• A 50 bp insertion (INDEL) varaint calling

  Answered 201 views 10 comments 0 points Most recent by Sheila June 2017Ask the GATK team
• UnifiedGenotyper command -o not found

  Answered 107 views 3 comments 0 points Most recent by Geraldine_VdAuwera June 2017Ask the GATK team
• SelectVariants According to AD Values

  Accepted Answer 188 views 1 comment 0 points Most recent by shlee February 2017Ask the GATK team
• --input-prior default value?

  Accepted Answer 464 views 6 comments 0 points Most recent by Geraldine_VdAuwera January 2017Ask the GATK team
• Higher concordance between genotypes representing reference homozygotes than other

  Accepted Answer 174 views 3 comments 0 points Most recent by Piotr December 2016Ask the GATK team
• Caller input_prior option

  Accepted Answer 326 views 8 comments 0 points Most recent by Geraldine_VdAuwera December 2016Ask the GATK team
• Bug in HaplotypeCaller: GT is called 0/1, but AD is 206,0

  Answered 1.3K views 20 comments 0 points Most recent by Sheila November 2016Ask the GATK team
• UnifiedGenotyper different results depending on the output mode

  Answered 338 views 5 comments 0 points Most recent by Sheila October 2016Ask the GATK team
• A question about a weird output of VCF file from UnitedGenotyper

  Answered 198 views 5 comments 0 points Most recent by Sheila August 2016Ask the GATK team
• Somehow the requested coordinate is not covered by the read?

  Accepted Answer 1.1K views 14 comments 0 points Most recent by Sheila August 2016Ask the GATK team
• Error when I called variants using flag "--output_mode EMIT_ALL_SITES" but only for one chromosome?

  Accepted Answer 195 views 4 comments 0 points Most recent by Sheila August 2016Ask the GATK team
• Unifiedgenotyper walker not found

  Answered 196 views 6 comments 0 points Most recent by Sheila July 2016Ask the GATK team
• Variant Calling by Unified Genotyper

  Answered 371 views 5 comments 0 points Most recent by Sheila July 2016Ask the GATK team
• HaplotypeCaller speed

  Answered 9.3K views 46 comments 1 point Most recent by Sheila July 2016Ask the GATK team
• GATK UnifiedGenotyper: calling "1/2" haplotypes

  Answered 224 views 1 comment 0 points Most recent by Geraldine_VdAuwera May 2016Ask the GATK team
• Which variant caller should be selected for my dataset?

  Answered 217 views 1 comment 0 points Most recent by Sheila May 2016Ask the GATK team
• HaplotypeCaller DP reports low values

  Answered 3.3K views 37 comments 1 point Most recent by Sheila May 2016Ask the GATK team
• Is HaplotypeCaller suitable for use in a GWAS project?

  Accepted Answer 402 views 6 comments 0 points Most recent by ianw May 2016Ask the GATK team
• Custom Info disappears after CombineVariants step

  Accepted Answer 233 views 0 comments 0 points Started by akmg May 2016 Ask the GATK team
• Counting number of reads affected by N's in CGIAR

  Answered 150 views 1 comment 0 points Most recent by Sheila April 2016Ask the GATK team
• UnifiedGenotyper multi-sample SNP calling

  Answered 279 views 1 comment 0 points Most recent by Sheila April 2016Ask the GATK team
• missing SNPs after gvcf combine and slow combination step

  Answered 592 views 6 comments 0 points Most recent by Geraldine_VdAuwera April 2016Ask the GATK team
• SNPs not supported by other evidence

  Answered 117 views 1 comment 0 points Most recent by Sheila April 2016Ask the GATK team
• Unified genotyper for less than 1 X coverage

  Accepted Answer 446 views 5 comments 0 points Most recent by Sheila March 2016Ask the GATK team
• (howto) Call variants with the UnifiedGenotyper

  Closed 5.8K views 11 comments 0 points Most recent by Sheila March 2016Tutorials
• In term of algorithms, what is the difference between haplotypecaller and unifiedgenotyper

  Answered 506 views 1 comment 0 points Most recent by Sheila March 2016Ask the GATK team
• does unifiedgenotyper also call genotype or just call variants?

  Answered 134 views 1 comment 0 points Most recent by Sheila March 2016Ask the GATK team
• Using the GATK Unified on a pooling sample

  Accepted Answer 379 views 4 comments 0 points Most recent by Hubert March 2016Ask the GATK team
• Multi-sample SNP calling with UnifiedGenotyper

  Accepted Answer 455 views 2 comments 0 points Most recent by aberry814 March 2016Ask the GATK team
• Unified Genotyper quality call

  Answered 494 views 21 comments 0 points Most recent by Sheila March 2016Ask the GATK team
• GATK 2.8.1 Unified Genotyper "Null alleles are not supported"

  Accepted Answer 782 views 18 comments 0 points Most recent by Geraldine_VdAuwera March 2016Ask the GATK team
• Singnification of an Error to run unified genotyper

  Accepted Answer 187 views 2 comments 0 points Most recent by Geraldine_VdAuwera March 2016Ask the GATK team
• unified genotyper vs. haplotype caller w/ pedigree study, major discrepancies

  Accepted Answer 808 views 10 comments 0 points Most recent by Sheila February 2016Ask the GATK team
• Empty VCF file from GATK-Lite UnifiedGenotyper

  Accepted Answer 2.1K views 30 comments 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• How does unified genotyper calculate prior probabilities for one sample?

  Answered 241 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• java error when using UnifiedGenotyper

  Accepted Answer 386 views 3 comments 0 points Most recent by npd75 January 2016Ask the GATK team
• Unified Genotyper Code exception - java.lang.IllegalArgumentException

  Answered 308 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2016Ask the GATK team
• How can I get UnifiedGenotyper to work on triploids

  Accepted Answer 529 views 9 comments 0 points Most recent by mschilling December 2015Ask the GATK team
• Generation of haplotype or phase data for SNPs in the flanking region of STRs

  504 views 3 comments 0 points Most recent by Geraldine_VdAuwera December 2015Ask the GATK team
• Error running GATK

  Accepted Answer 664 views 5 comments 0 points Most recent by Sheila November 2015Ask the GATK team
• Discrepancies between HC and UG during Known Variant Bootstrapping

  Accepted Answer 486 views 14 comments 0 points Most recent by Geraldine_VdAuwera November 2015Ask the GATK team
• ploidy level in UnifiedGenotyper

  Accepted Answer 294 views 1 comment 0 points Most recent by Sheila November 2015Ask the GATK team
• variant calling by unified genotyper

  Accepted Answer 253 views 3 comments 0 points Most recent by Geraldine_VdAuwera October 2015Ask the GATK team
• Can a SNP with 35 vs 54 reads really be homozygous?

  Accepted Answer 162 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015Ask the GATK team
• UnifiedGenotyper gets hung waiting for file lock

  Accepted Answer 5.8K views 24 comments 1 point Most recent by Geraldine_VdAuwera October 2015Ask the GATK team
• Should the number of SNPs stop changing between successive rounds of BSQR?

  Accepted Answer 243 views 1 comment 0 points Most recent by Geraldine_VdAuwera October 2015Ask the GATK team
• Variant calls being missed - how to improve variant detection using Sanger sequencing data?

  1K views 10 comments 0 points Most recent by Sheila September 2015Ask the GATK team
• Haploid genomes

  Accepted Answer 2.8K views 18 comments 0 points Most recent by Sheila September 2015Ask the GATK team
• General variant detection pipeline

  Accepted Answer 263 views 1 comment 0 points Most recent by Sheila August 2015Ask the GATK team
• EMIT_ALL_CONFIDENT_SITES option, omitting non-'LowQual' sites

  Answered 491 views 14 comments 0 points Most recent by Geraldine_VdAuwera August 2015Ask the GATK team
• invariant calls not consistently included in Unififed Genotyper output

  Answered 314 views 14 comments 0 points Most recent by amsci8 July 2015Ask the GATK team
• Why do you have to provide -I and -L if GENOTYPE_GIVEN_ALLELES is used: UnifiedGenotyper

  Accepted Answer 1.1K views 5 comments 1 point Most recent by tommycarstensen July 2015Ask the GATK team
• Unified Genotyper gets stuck

  Answered 288 views 5 comments 0 points Most recent by Sheila July 2015Ask the GATK team
• UnifiedGenotyper pooled:how to set the minimum number of reads supporting an alternate allele

  Accepted Answer 598 views 4 comments 1 point Most recent by Geraldine_VdAuwera July 2015Ask the GATK team
• How Unified Genotyper works - RETIRED

  Closed 18.5K views 100 comments 0 points Most recent by vasilis June 2015Archive
• StrandOddsRatio computation

  Accepted Answer 933 views 8 comments 1 point Most recent by manon_sourdeix June 2015Ask the GATK team
• GATK's UnifiedGenotyper SNP/Indel Calling Producing No Results

  Answered 1.1K views 8 comments 0 points Most recent by zzy June 2015Ask the GATK team
• CombineVariants unwanted merge behaviour at identical positions

  Accepted Answer 607 views 4 comments 0 points Most recent by Geraldine_VdAuwera June 2015Ask the GATK team
• variant detection: DP and Mendelization

  Accepted Answer 233 views 1 comment 0 points Most recent by Sheila May 2015Ask the GATK team
• Is it possible to disable DuplicateReadFilter in UnifiedGenotyper?

  Accepted Answer 467 views 2 comments 0 points Most recent by Geraldine_VdAuwera May 2015Ask the GATK team
• How to estimate heap size (-Xmx) necessary to call variants using Unified Genotyper?

  Accepted Answer 1.5K views 11 comments 0 points Most recent by Geraldine_VdAuwera May 2015Ask the GATK team
• Questions about the UnifiedGenotyper Queue script

  Accepted Answer 549 views 7 comments 0 points Most recent by ziva May 2015Ask the GATK team
• UnifiedGenotyper: Multiple variants with the same coordinate?

  Accepted Answer 319 views 2 comments 0 points Most recent by antoinetonio May 2015Ask the GATK team
• Bug in various tools, 2.4-7 : "ArrayIndexOutOfBoundsException"

  2.3K views 36 comments 1 point Most recent by Sheila April 2015Announcements
• Unified Genotyper settings for 200 half-sibs

  Accepted Answer 230 views 2 comments 0 points Most recent by tommycarstensen March 2015Ask the GATK team
• UnifiedGenotyper crashes: HAPLOTYPE_MAX_LENGTH must be > 0 but got 0

  Accepted Answer 353 views 3 comments 0 points Most recent by Rebecca March 2015Ask the GATK team
• incompatible chromosome coordinates in dbsnp and reference file for UnifiedGenotyper

  303 views 2 comments 0 points Most recent by max_shpak March 2015Ask the GATK team
• Incorrect Heterozygotic Call

  Answered 170 views 1 comment 0 points Most recent by Geraldine_VdAuwera March 2015Ask the GATK team
• "Overcalling" deletion in UnifiedGenotyper GENOTYPE_GIVEN_ALLELES mode

  Answered 297 views 7 comments 0 points Most recent by tommycarstensen March 2015Ask the GATK team
• variant analysis -calling

  Accepted Answer 192 views 1 comment 0 points Most recent by pdexheimer February 2015Ask the GATK team
• Inconsistent DP within a site in vcf

  Accepted Answer 215 views 1 comment 0 points Most recent by Geraldine_VdAuwera February 2015Ask the GATK team
• --input_prior (UG)

  Answered 219 views 2 comments 0 points Most recent by Blue February 2015Ask the GATK team
• Position of Indel event based on the REF

  Accepted Answer 690 views 5 comments 0 points Most recent by Sheila February 2015Ask the GATK team
• Overlapping positions

  Answered 468 views 5 comments 0 points Most recent by tommycarstensen February 2015Ask the GATK team
• UG call combined SNP/INDEL sites in GGA mode?

  Accepted Answer 348 views 1 comment 0 points Most recent by Geraldine_VdAuwera January 2015Ask the GATK team
• HaplotypeScore as an annotation for VariantRecalibrator after UnifiedGenotyper

  Accepted Answer 278 views 2 comments 0 points Most recent by Geraldine_VdAuwera January 2015Ask the GATK team