liguowang CrossMap issues

liguowang / CrossMap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

https://crossmap.readthedocs.io/en/latest/

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issues

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Failed to map entries with no explanation

#72 PeterSu92 opened 1 month ago
5
CrossMap.py bam gives AttributeError: 'dict' object has no attribute 'to_dict'

#71 katlande closed 1 month ago
1
CrossMap breaks VCF by replacing "*" genotype with a duplicate variant allele

#70 gnxsf opened 2 months ago
4
meaning of viewchain output and strand information

#69 euffelmann closed 3 months ago
2
MAF liftover resulting in same reference and alternate allele

#68 skanwal opened 4 months ago
7
Installing v0.7.0 makes python 3.11 coredump when help('modules') is called

#67 t-kreitler opened 5 months ago
2
Redundancy in these lines from mapvcf.py if "no-comp-allele" option is turned on?

#66 lwtan90 opened 5 months ago
1
Don't understand the meaning of "no-comp-alleles"

#65 lwtan90 opened 5 months ago
1
command not found: CrossMap

#64 skanwal closed 5 months ago
2
gvcf KeyError: '>'

#63 solivehong opened 7 months ago
6
CrossMap v0.6.5 KeyError: "-"

#62 boseb closed 6 months ago
2
CrossMap does not install into site-packages folder

#61 romunov closed 9 months ago
1
Issue with liftover of vcf file from T2T to hg38

#60 Taghrid-M opened 1 year ago
3
A rust implementation of CrossMap

#59 wjwei-handsome opened 1 year ago
2
AttributeError: 'NoneType' object has no attribute 'replace'

#58 hermes1130 opened 1 year ago
2
License

#57 anders-lgi opened 1 year ago
0
Fails to map many variants when using VCF option

#56 jpuntomarcos opened 1 year ago
2
Error Running CrossMap in Mac Terminal for VCF

#55 o0stsou0o opened 1 year ago
2
Installing CrossMap on Mac Issues

#54 o0stsou0o closed 1 year ago
0
Wrong ALT when lifting over ALT=T,* like variants

#53 maxrossi91 opened 1 year ago
2
Unable to convert hg19 to hg38 in bed file. And not taking optional arguments

#52 jporton opened 1 year ago
1
Crossmap throws error while lifting over from MAF file

#51 Subhi closed 1 year ago
1
Convert VCF format files, KeyError: '>' in CrossMap 0.6.4

#50 rmozafari closed 1 year ago
4
Erroneous SAM flags introduced in version 0.6.3

#49 jeizenga opened 2 years ago
5
IndexError: string index out of range

#48 Z-Zen closed 2 years ago
1
Unexpected mapping where a deletion turns into a SNP

#47 ivan-mh closed 2 years ago
4
vcf failed in python 3.10

#46 aitgon closed 2 years ago
3
Error: KeyError: '>', version=0.6.1,I want to know it

#45 mofisl closed 2 years ago
1
Wrong last stable nucleotide for a deletion in GRCh37 to GRCh38 conversion

#44 ivan-mh opened 2 years ago
55
CrossMap VCF KeyError: '>'

#43 ew367 closed 2 years ago
1
UnboundLocalError: local variable 'chr_template' referenced before assignment

#42 WZo0o closed 2 years ago
1
Fix an err msg typo

#41 ccneko closed 2 years ago
0
CrossMap VCF header entries do not work with Bcftools

#40 gungorbudak closed 2 years ago
1
Wrong mapping when conversion from GRCh38 to GRCh37

#39 samuellawty closed 2 years ago
3
Maybe a bug on version 0.6.0

#38 nemesis-lab opened 2 years ago
4
Is it suitable for plants？

#37 pjx1990 closed 2 years ago
1
list index out of range

#36 ruizhideng closed 2 years ago
11
CrossMap v0.5.4 outputs fake data when it failed to convert the data.

#35 monagai opened 2 years ago
0
Removed some repos that don't belong into a repo.

#34 erikbgithub opened 2 years ago
0
Many continuous regions have been splitted into many regions

#33 ShixiangWang closed 2 years ago
1
4/16/2021: Release version 0.5.3/0.5.4

#32 Shicheng-Guo opened 2 years ago
2
Protocol for hg19 PLINK (BED/BIM/FAM) to hg38 PLINK (BED/BIM/FAM)

#31 Shicheng-Guo opened 2 years ago
0
convert bigwig error

#30 jiangshan529 closed 1 year ago
6
REF==ALT for variants with ALT as major

#29 cindywen96 opened 3 years ago
2
'chr' issue in converting bigWig files

#28 joshtburdick closed 3 years ago
3
Double Alt Heterozygous Variant

#27 PabloBotas opened 3 years ago
0
add bioconda and Galaxy badge

#26 bgruening closed 2 years ago
0
Does not convert ALT field in structural variant VCFs

#25 ManavalanG opened 3 years ago
6
Recent Crossmap version is not available in bioconda

#24 ManavalanG opened 3 years ago
1
Option to not change reference allele when liftovering vcf files

#23 dwuab closed 3 years ago
2