Issues

• No SVTYPE=INV in AGGREGATED SVMODEL

  DecodeGenetics/graphtyper#171 · Filter by author zuyan413 opened on Jan 19, 2026

• merge bams issue

  DecodeGenetics/graphtyper#170 · Filter by author xuefenfei712 opened on Jan 12, 2026
  1

• When calling and genotyping SVs among very closely related populations, the false positive rate is very high.

  DecodeGenetics/graphtyper#169 · Filter by author kuangzhuoran opened on Dec 31, 2025
  2

• Recommended FT filter parameters

  DecodeGenetics/graphtyper#168 · Filter by author zhujiahua700403 opened on Nov 3, 2025

• Negative count in genotype output of Graphtyper genotype_sv

  DecodeGenetics/graphtyper#167 · Filter by author sroener opened on Aug 7, 2025
  4

• Graphtyper vcf_merge failing with error code 139 for VCFs containing SVs

  DecodeGenetics/graphtyper#166 · Filter by author sroener opened on Aug 4, 2025
  8

• adding new samples to already generated vcf files of SNPs

  DecodeGenetics/graphtyper#165 · Filter by author BioInf2305 opened on Jul 1, 2025
  1

• SV genotyping: Multiple BAMs for single sample

  DecodeGenetics/graphtyper#164 · Filter by author tgong1 opened on May 20, 2025
  1

• Pre-processing alignments with bamshrink before genotyping with --no_bamshrink

  DecodeGenetics/graphtyper#163 · Filter by author malthesr opened on Mar 21, 2025
  5

• Scalable Genotyping for Large Cohorts

  DecodeGenetics/graphtyper#162 · Filter by author ytt01 opened on Mar 5, 2025

• can some argument change the criteria to obtain high-confidence SV genotype call with low coverage NGS data?

  DecodeGenetics/graphtyper#161 · Filter by author liuqi-C opened on Feb 26, 2025

• Genotype difference between Graphtyper & SURVIVOR

  DecodeGenetics/graphtyper#160 · Filter by author Sreelekshmi-291 opened on Feb 20, 2025
  1

• Graphtyper copying the same files multiple times if using "--region_file"

  DecodeGenetics/graphtyper#159 · Filter by author sroener opened on Jan 7, 2025
  2

• question about “--sams=bam.list”

  DecodeGenetics/graphtyper#157 · Filter by author Henry-Ding opened on Nov 8, 2024
  8

• graphtyper genotype produces too many files for graphtyper vcf_concatenate to combine

  DecodeGenetics/graphtyper#156 · Filter by author zachary-foster opened on Oct 17, 2024
  1

• Not able to handle missing sites

  DecodeGenetics/graphtyper#154 · Filter by author Hjorvik opened on Aug 1, 2024
  1

• Genotype_sv Aggregate model has less Output SVs than Input SVs

  DecodeGenetics/graphtyper#152 · Filter by author ghost opened on Jul 23, 2024
  1

• HLA-Genotyping: <error> Converting "HLA-A*01:01:01:01" of size 17 to int failed

  DecodeGenetics/graphtyper#151 · Filter by author ghost opened on May 20, 2024
  3

• Created chopped CRAI

  DecodeGenetics/graphtyper#150 · Filter by author nathanLauHKGI opened on May 17, 2024
  2

• ( AC / NUM_MERGED_SVS ) < 25

  DecodeGenetics/graphtyper#149 · Filter by author weizhu365 opened on Mar 28, 2024
  2

• vcf_merge for SV

  DecodeGenetics/graphtyper#148 · Filter by author JoannaTan opened on Mar 25, 2024
  1

• Is it possible to call STRs with graphtyper?

  DecodeGenetics/graphtyper#147 · Filter by author scienception opened on Mar 20, 2024
  1

• In the genotype_sv result, the REF filed is N, and the ALT filed is not a sequence.

  DecodeGenetics/graphtyper#146 · Filter by author tanger-code opened on Jan 24, 2024
  3

• Graphtyper for calling human X-chromosome variants

  DecodeGenetics/graphtyper#145 · Filter by author Sirtx opened on Jan 17, 2024

• REF in VCF file is N

  DecodeGenetics/graphtyper#144 · Filter by author pingxinxing opened on Dec 4, 2023
  2