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freeseek
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gtc2vcf
Tools to convert Illumina IDAT/BPM/EGT/GTC and Affymetrix CEL/CHP files to VCF
MIT License
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Updating the conda environment
#78
rajwanir
opened
1 month ago
6
Is it possible to resolve multi-nucleotide variants (MNV) to biallelic records?
#77
rajwanir
opened
1 month ago
7
Records represented as [D/I] in manifest.
#76
rajwanir
opened
3 months ago
10
Couple SNPs on ChrY and ChrM shifted by -1.
#75
rajwanir
closed
3 months ago
2
Drop marker if SourceSeq maps to different loci equally well.
#74
rajwanir
opened
3 months ago
3
Indel left-normalized within gtc2vcf by default? Options to turn this off?
#73
rajwanir
closed
3 months ago
4
Pseudo-autosomal regions (PAR).
#72
rajwanir
opened
4 months ago
1
Multi allelic records
#71
rajwanir
closed
4 months ago
4
Error while running linsolve1
#70
teepean
opened
4 months ago
1
Add an explicit FORMAT/TAG for illumina genotype?
#69
rajwanir
opened
5 months ago
3
ALLELE_A and ALLELE_B encoding in the VCF?
#68
rajwanir
opened
5 months ago
4
bpm with an alternate reference csv_manifest simultanously?
#67
rajwanir
closed
5 months ago
2
Error while running linsolve1
#66
Dazcam
closed
4 months ago
4
Loci skipped with SourceSeq mapping.
#65
rajwanir
opened
7 months ago
1
CNV and coordinates mapping issue?
#64
rajwanir
opened
7 months ago
1
Any suggestions on handling manifests with missing RefStrand and SourceSeq columns?
#63
rajwanir
closed
4 months ago
8
Unexpected Error: uncaught exception
#62
Tianwen-lab-star
opened
8 months ago
2
Recommended filtering
#61
iranmdl
closed
10 months ago
11
Segfault with cel-files not succesful.
#60
teepean
opened
10 months ago
1
Error Encountered while parsing the input
#59
crbeam
opened
1 year ago
2
Affy2vcf snp-posterior file
#58
IPriscilla
opened
1 year ago
9
empty vcf final file
#57
sgomes-catarina
closed
1 year ago
3
Input not detected as vcf or bcf format
#56
cantlap
closed
1 year ago
3
Final BCF not being created.
#55
mahaaamir
closed
1 year ago
5
vcf file blank
#54
dtzhu337
closed
1 year ago
1
bioconda
#53
lightning-auriga
closed
1 year ago
0
Error for installing AutoConvert
#52
hyunnnie
closed
1 year ago
1
plink matrix format
#51
gevro
closed
2 years ago
6
VCF lines lacking GT tag
#50
kasia-te
closed
1 year ago
2
Failed to open file "Ou" : No such file or directory
#49
crbeam
closed
1 year ago
1
GTC files cannot be listed through both command interface and file list when only submitting a .txt file
#48
hsmith9002
closed
2 years ago
4
vcf files not being saved
#47
mahaaamir
closed
2 years ago
3
idat or gtc in command line
#46
jeantristanb
closed
1 year ago
1
gtc2vcf cannot open gtc files
#45
mahaaamir
closed
2 years ago
1
ERROR in converting CHP to VCF
#44
lizhan96
closed
1 year ago
1
how to convert CEL to CHP?
#43
lizhan96
closed
1 year ago
2
How to get Call_Freq, AAfreq, BBfreq, and AB Freq
#42
mansi800
closed
1 year ago
0
Feature request: alternative genome reference for --genome-studio input
#41
robkar
closed
1 year ago
0
No output files generated for Illunmina reports
#40
rashindrie
closed
3 years ago
15
Genomestudio file to vcf
#39
PriscillaPoemba
closed
3 years ago
11
affy2vcf: How to make the IDs of generated vcf files be rsid from annotation files given by Affymetrix but not probeset id?
#38
YuquanW
closed
3 years ago
2
compressed VCF
#37
Ballote
closed
2 years ago
2
No output VCF files
#36
Ballote
closed
3 years ago
7
Citation
#35
xsun1229
closed
3 years ago
1
Some installation issues
#34
xsun1229
closed
3 years ago
7
Question affy2vcf
#33
ghost
closed
2 years ago
2
build in macOS
#32
sinamajidian
closed
3 years ago
1
Error: Too many open files
#31
QidiFeng
closed
3 years ago
0
NORMX/NORMY/R/THETA missing from GenomeStudio text output
#30
robkar
closed
3 years ago
0
Error in names(object) <- nm gtc2vcf_plot.R
#29
PriscillaPoemba
closed
3 years ago
5
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