Illumina GTCtoVCF issues

Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF

Apache License 2.0

41 stars 31 forks source link

issues

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Empty ALT genotypes?

#81 rajwanir opened 2 months ago
1
Tool assumptions and behaviour

#80 rajwanir opened 3 months ago
6
updates link from ACLI to DRAGEN Array

#79 jzieve closed 3 months ago
0
Any workaround for missing RefStrand and SourceSeq column in the manifest?

#78 rajwanir closed 3 months ago
7
SB calculation

#77 marissa97 opened 12 months ago
1
Any experience about GQ settings

#76 AliceCheng7 opened 1 year ago
1
adds semi-archived message to README

#75 jzieve closed 1 year ago
0
Now supports extracting gencall scores (GCALL) as real numbers

#74 Ahhgust opened 1 year ago
5
Docker container

#73 stephenturner closed 2 years ago
5
ERROR - Reference is missing entry for chromosome 3

#72 HoneeeyBee closed 2 years ago
2
Python3 support

#71 Stikus opened 2 years ago
1
Readme py2 req

#70 jjzieve closed 2 years ago
3
VCF REF column outputting in bytes instead of string

#69 rarsenal closed 2 years ago
3
GQ score clarification

#68 Derrup opened 3 years ago
3
Bus error when converting GTC to VCF

#67 khzhu closed 3 years ago
7
SourceSeq validation failures should be skipped instead of erroring out

#66 jjzieve opened 3 years ago
0
Python3 Question

#65 tbrunetti closed 4 years ago
3
Reference not detected if lowercase characters

#64 BiKC opened 4 years ago
4
Master

#63 jjzieve closed 4 years ago
0
download_reference script has broken links

#62 jjzieve closed 4 years ago
2
Release/1.2.1

#61 jjzieve closed 4 years ago
0
Next release

#60 varuna-sd closed 4 years ago
2
Unclear Error message

#59 brianyiktaktsui opened 4 years ago
1
Handles case where indels with opposite orientation (e.g. [I/D] vs. […

#58 jjzieve closed 4 years ago
0
Bug/baf mnv handling

#57 jjzieve closed 4 years ago
0
Addresses case where ALT allele(s) are one base, hence an indel and n…

#56 jjzieve closed 4 years ago
0
Unable to run download_reference.sh on Mac

#55 biying-orig3n closed 4 years ago
3
download_reference.sh is outdated

#54 moranr7 closed 4 years ago
3
Feature/change gq type

#53 jjzieve closed 4 years ago
1
Feature/change gq type

#52 jjzieve closed 4 years ago
0
GQ type is "String" instead of "Float"

#51 kmhernan closed 4 years ago
1
Replace ID in output VCF with `--id` option

#50 stephenturner opened 4 years ago
0
Illumina Generated Manifest has no RefStrand column

#49 tbrunetti opened 4 years ago
5
GTC parser error : All GT values in converted vcf are './.'

#48 gezthxbio closed 5 years ago
4
Applies change from BeadArrayFiles repository

#47 jjzieve closed 4 years ago
0
Merge pull request #44 from Illumina/release/1.2.0

#46 jjzieve closed 5 years ago
0
Release/1.2.0

#45 jjzieve closed 5 years ago
0
Release/1.2.0

#44 jjzieve closed 5 years ago
3
Version 1.2.0

#43 jjzieve closed 5 years ago
1
Precision difference when updating numpy versions

#42 jjzieve opened 5 years ago
0
Additional fields

#41 jjzieve closed 5 years ago
9
Add dockerfile

#40 jjzieve closed 2 years ago
1
Uses GNU and OSX compatible mktemp

#39 jjzieve closed 4 years ago
1
GTC converter - WARNING - Reference is missing entry for chromosomes

#38 cbiOPela opened 5 years ago
8
.vcf format for BaseSpace Variant Interpreter?

#37 cbiOPela closed 5 years ago
0
Update download_reference.sh

#36 GvandeSteeg closed 5 years ago
1
scripts/download_reference.sh fails when missing `realpath`

#35 GvandeSteeg closed 5 years ago
0
Typo in comment on BPMRecord

#34 eyherabh closed 5 years ago
0
Possible error in comment on last test

#33 eyherabh closed 5 years ago
0
About ImportError: No module named vcf.parser

#32 JeonHyungJin closed 5 years ago
5