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37 Open 34 Closed
37 Open 34 Closed
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Issues list

Coordinate Conversion Before/After Variant Calling?
#78 opened Oct 18, 2024 by DayTimeMouse
2
Regarding output of the file generated
#77 opened Sep 17, 2024 by Proy321
2
--chromid a (as-is) behavior is more like "match query" than "as-is" and causes problems under certain conditions
#74 opened Jul 24, 2024 by pickettbd
bed parsing is too rigid for 12 or 20 columns and files with 13-19 or 21+ columns are ignored
#73 opened Jul 24, 2024 by pickettbd
Failed to map entries with no explanation
#72 opened May 13, 2024 by PeterSu92
5
CrossMap breaks VCF by replacing "*" genotype with a duplicate variant allele
#70 opened Apr 22, 2024 by gnxsf
7
MAF liftover resulting in same reference and alternate allele
#68 opened Feb 26, 2024 by skanwal
7
Installing v0.7.0 makes python 3.11 coredump when help('modules') is called
#67 opened Jan 30, 2024 by t-kreitler
2
Redundancy in these lines from mapvcf.py if "no-comp-allele" option is turned on?
#66 opened Jan 23, 2024 by lwtan90
1
Don't understand the meaning of "no-comp-alleles"
#65 opened Jan 22, 2024 by lwtan90
1
Issue with liftover of vcf file from T2T to hg38
#60 opened Jun 6, 2023 by Taghrid-M
3
A rust implementation of CrossMap
#59 opened Apr 13, 2023 by wjwei-handsome
2
AttributeError: 'NoneType' object has no attribute 'replace'
#58 opened Mar 25, 2023 by hermes1130
2
License
#57 opened Mar 24, 2023 by anders-lgi
Fails to map many variants when using VCF option
#56 opened Feb 9, 2023 by jpuntomarcos
2
Error Running CrossMap in Mac Terminal for VCF
#55 opened Jan 31, 2023 by o0stsou0o
2
Wrong ALT when lifting over ALT=T,* like variants
#53 opened Dec 1, 2022 by maxrossi91
2
Unable to convert hg19 to hg38 in bed file. And not taking optional arguments
#52 opened Nov 23, 2022 by jporton
1
Erroneous SAM flags introduced in version 0.6.3
#49 opened Jun 15, 2022 by jeizenga
5
Wrong last stable nucleotide for a deletion in GRCh37 to GRCh38 conversion
#44 opened Feb 17, 2022 by ivan-mh
55
Maybe a bug on version 0.6.0
#38 opened Nov 23, 2021 by nemesis-lab
4
CrossMap v0.5.4 outputs fake data when it failed to convert the data.
#35 opened Sep 6, 2021 by monagai
4/16/2021: Release version 0.5.3/0.5.4
#32 opened Aug 7, 2021 by Shicheng-Guo
2
Protocol for hg19 PLINK (BED/BIM/FAM) to hg38 PLINK (BED/BIM/FAM)
#31 opened Jul 23, 2021 by Shicheng-Guo
REF==ALT for variants with ALT as major
#29 opened Apr 30, 2021 by cindywen96
2
ProTip! Follow long discussions with comments:>50.