Issues

• lifting-over hap2 to hap1 coordinates of a T2T genome

  liguowang/CrossMap#84 · Filter by author Overcraft90 opened on Mar 26, 2026

• Empty alternate allele after liftOver with CrossMap

  liguowang/CrossMap#83 · Filter by author garyzhubc opened on Oct 14, 2025
  8

• No change of chromosomal position with liftover on VCF

  liguowang/CrossMap#81 · Filter by author Mannyari opened on Jul 31, 2025

• MAF insertions are broken after liftover

  liguowang/CrossMap#80 · Filter by author dheiman opened on May 23, 2025

• Coordinate Conversion Before/After Variant Calling?

  liguowang/CrossMap#78 · Filter by author DayTimeMouse opened on Oct 18, 2024
  2

• Regarding output of the file generated

  liguowang/CrossMap#77 · Filter by author Proy321 opened on Sep 17, 2024
  2

• --chromid a (as-is) behavior is more like "match query" than "as-is" and causes problems under certain conditions

  liguowang/CrossMap#74 · Filter by author pickettbd opened on Jul 24, 2024

• bed parsing is too rigid for 12 or 20 columns and files with 13-19 or 21+ columns are ignored

  liguowang/CrossMap#73 · Filter by author pickettbd opened on Jul 24, 2024

• Failed to map entries with no explanation

  liguowang/CrossMap#72 · Filter by author PeterSu92 opened on May 13, 2024
  5

• CrossMap breaks VCF by replacing "*" genotype with a duplicate variant allele

  liguowang/CrossMap#70 · Filter by author gnxsf opened on Apr 22, 2024
  8

• MAF liftover resulting in same reference and alternate allele

  liguowang/CrossMap#68 · Filter by author skanwal opened on Feb 26, 2024
  7

• Installing v0.7.0 makes python 3.11 coredump when help('modules') is called

  liguowang/CrossMap#67 · Filter by author t-kreitler opened on Jan 30, 2024
  2

• Redundancy in these lines from mapvcf.py if "no-comp-allele" option is turned on?

  liguowang/CrossMap#66 · Filter by author lwtan90 opened on Jan 23, 2024
  1

• Don't understand the meaning of "no-comp-alleles"

  liguowang/CrossMap#65 · Filter by author lwtan90 opened on Jan 22, 2024
  5

• Issue with liftover of vcf file from T2T to hg38

  liguowang/CrossMap#60 · Filter by author Taghrid-M opened on Jun 6, 2023
  3

• A rust implementation of CrossMap

  liguowang/CrossMap#59 · Filter by author wjwei-handsome opened on Apr 13, 2023
  2

• AttributeError: 'NoneType' object has no attribute 'replace'

  liguowang/CrossMap#58 · Filter by author hermes1130 opened on Mar 25, 2023
  2

• License

  liguowang/CrossMap#57 · Filter by author anders-lgi opened on Mar 24, 2023

• Fails to map many variants when using VCF option

  liguowang/CrossMap#56 · Filter by author jpuntomarcos opened on Feb 9, 2023
  2

• Error Running CrossMap in Mac Terminal for VCF

  liguowang/CrossMap#55 · Filter by author o0stsou0o opened on Jan 31, 2023
  2

• Wrong ALT when lifting over ALT=T,* like variants

  liguowang/CrossMap#53 · Filter by author maxrossi91 opened on Dec 1, 2022
  2

• Unable to convert hg19 to hg38 in bed file. And not taking optional arguments

  liguowang/CrossMap#52 · Filter by author jporton opened on Nov 23, 2022
  1

• Erroneous SAM flags introduced in version 0.6.3

  liguowang/CrossMap#49 · Filter by author jeizenga opened on Jun 15, 2022
  5

• Wrong last stable nucleotide for a deletion in GRCh37 to GRCh38 conversion

  liguowang/CrossMap#44 · Filter by author ghost opened on Feb 17, 2022
  59

• Maybe a bug on version 0.6.0

  liguowang/CrossMap#38 · Filter by author nemesis-lab opened on Nov 23, 2021
  4