illumina/gtctovcf issues and pull requests

#81 - Empty ALT genotypes?

Issue - State: open - Opened by rajwanir 10 months ago - 1 comment

#80 - Tool assumptions and behaviour

Issue - State: open - Opened by rajwanir 11 months ago - 6 comments

#80 - Tool assumptions and behaviour

Issue - State: open - Opened by rajwanir 11 months ago - 6 comments

#79 - updates link from ACLI to DRAGEN Array

Pull Request - State: closed - Opened by jzieve 11 months ago

#79 - updates link from ACLI to DRAGEN Array

Pull Request - State: closed - Opened by jzieve 11 months ago

#78 - Any workaround for missing RefStrand and SourceSeq column in the manifest?

Issue - State: closed - Opened by rajwanir 11 months ago - 7 comments

#78 - Any workaround for missing RefStrand and SourceSeq column in the manifest?

Issue - State: closed - Opened by rajwanir 11 months ago - 7 comments

#77 - SB calculation

Issue - State: open - Opened by marissa97 over 1 year ago - 1 comment

#77 - SB calculation

Issue - State: open - Opened by marissa97 over 1 year ago - 1 comment

#76 - Any experience about GQ settings

Issue - State: open - Opened by AliceCheng7 almost 2 years ago - 1 comment

#76 - Any experience about GQ settings

Issue - State: open - Opened by AliceCheng7 almost 2 years ago - 1 comment

#75 - adds semi-archived message to README

Pull Request - State: closed - Opened by jzieve almost 2 years ago

#75 - adds semi-archived message to README

Pull Request - State: closed - Opened by jzieve almost 2 years ago

#74 - Now supports extracting gencall scores (GCALL) as real numbers

Pull Request - State: open - Opened by Ahhgust almost 2 years ago - 5 comments

#74 - Now supports extracting gencall scores (GCALL) as real numbers

Pull Request - State: open - Opened by Ahhgust almost 2 years ago - 5 comments

#73 - Docker container

Pull Request - State: closed - Opened by stephenturner almost 3 years ago - 5 comments

#73 - Docker container

Pull Request - State: closed - Opened by stephenturner almost 3 years ago - 5 comments

#72 - ERROR - Reference is missing entry for chromosome 3

Issue - State: closed - Opened by HoneeeyBee about 3 years ago - 2 comments

#72 - ERROR - Reference is missing entry for chromosome 3

Issue - State: closed - Opened by HoneeeyBee about 3 years ago - 2 comments

#71 - Python3 support

Issue - State: open - Opened by Stikus over 3 years ago - 1 comment

#71 - Python3 support

Issue - State: open - Opened by Stikus over 3 years ago - 1 comment

#70 - Readme py2 req

Pull Request - State: closed - Opened by jjzieve over 3 years ago - 3 comments

#69 - VCF REF column outputting in bytes instead of string

Issue - State: closed - Opened by rarsenal over 3 years ago - 3 comments

#69 - VCF REF column outputting in bytes instead of string

Issue - State: closed - Opened by rarsenal over 3 years ago - 3 comments

#68 - GQ score clarification

Issue - State: open - Opened by Derrup over 4 years ago - 3 comments

#68 - GQ score clarification

Issue - State: open - Opened by Derrup over 4 years ago - 3 comments

#67 - Bus error when converting GTC to VCF

Issue - State: closed - Opened by khzhu over 4 years ago - 7 comments

#67 - Bus error when converting GTC to VCF

Issue - State: closed - Opened by khzhu over 4 years ago - 7 comments

#66 - SourceSeq validation failures should be skipped instead of erroring out

Issue - State: open - Opened by jjzieve over 4 years ago
Labels: bug

#66 - SourceSeq validation failures should be skipped instead of erroring out

Issue - State: open - Opened by jjzieve over 4 years ago
Labels: bug

#65 - Python3 Question

Issue - State: closed - Opened by tbrunetti over 4 years ago - 3 comments

#65 - Python3 Question

Issue - State: closed - Opened by tbrunetti over 4 years ago - 3 comments

#64 - Reference not detected if lowercase characters

Issue - State: open - Opened by BiKC over 4 years ago - 4 comments
Labels: question

#64 - Reference not detected if lowercase characters

Issue - State: open - Opened by BiKC over 4 years ago - 4 comments
Labels: question

#63 - Master

Pull Request - State: closed - Opened by jjzieve almost 5 years ago

#62 - download_reference script has broken links

Issue - State: closed - Opened by jjzieve almost 5 years ago - 2 comments

#61 - Release/1.2.1

Pull Request - State: closed - Opened by jjzieve almost 5 years ago

#60 - Next release

Issue - State: closed - Opened by varuna-sd almost 5 years ago - 2 comments

#59 - Unclear Error message

Issue - State: open - Opened by brianyiktaktsui about 5 years ago - 1 comment
Labels: bug

#59 - Unclear Error message

Issue - State: open - Opened by brianyiktaktsui about 5 years ago - 1 comment
Labels: bug

#58 - Handles case where indels with opposite orientation (e.g. [I/D] vs. […

Pull Request - State: closed - Opened by jjzieve about 5 years ago

#58 - Handles case where indels with opposite orientation (e.g. [I/D] vs. […

Pull Request - State: closed - Opened by jjzieve about 5 years ago

#57 - Bug/baf mnv handling

Pull Request - State: closed - Opened by jjzieve about 5 years ago

#57 - Bug/baf mnv handling

Pull Request - State: closed - Opened by jjzieve about 5 years ago

#56 - Addresses case where ALT allele(s) are one base, hence an indel and n…

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#56 - Addresses case where ALT allele(s) are one base, hence an indel and n…

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#55 - Unable to run download_reference.sh on Mac

Issue - State: closed - Opened by biying-orig3n over 5 years ago - 3 comments

#54 - download_reference.sh is outdated

Issue - State: closed - Opened by moranr7 over 5 years ago - 3 comments

#54 - download_reference.sh is outdated

Issue - State: closed - Opened by moranr7 over 5 years ago - 3 comments

#53 - Feature/change gq type

Pull Request - State: closed - Opened by jjzieve over 5 years ago - 1 comment

#53 - Feature/change gq type

Pull Request - State: closed - Opened by jjzieve over 5 years ago - 1 comment

#52 - Feature/change gq type

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#52 - Feature/change gq type

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#51 - GQ type is "String" instead of "Float"

Issue - State: closed - Opened by kmhernan over 5 years ago - 1 comment

#51 - GQ type is "String" instead of "Float"

Issue - State: closed - Opened by kmhernan over 5 years ago - 1 comment

#50 - Replace ID in output VCF with `--id` option

Issue - State: open - Opened by stephenturner over 5 years ago
Labels: enhancement

#50 - Replace ID in output VCF with `--id` option

Issue - State: open - Opened by stephenturner over 5 years ago
Labels: enhancement

#49 - Illumina Generated Manifest has no RefStrand column

Issue - State: open - Opened by tbrunetti over 5 years ago - 5 comments
Labels: question

#49 - Illumina Generated Manifest has no RefStrand column

Issue - State: open - Opened by tbrunetti over 5 years ago - 5 comments
Labels: question

#48 - GTC parser error : All GT values in converted vcf are './.'

Issue - State: closed - Opened by gezthxbio over 5 years ago - 4 comments

#48 - GTC parser error : All GT values in converted vcf are './.'

Issue - State: closed - Opened by gezthxbio over 5 years ago - 4 comments

#47 - Applies change from BeadArrayFiles repository

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#47 - Applies change from BeadArrayFiles repository

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#46 - Merge pull request #44 from Illumina/release/1.2.0

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#45 - Release/1.2.0

Pull Request - State: closed - Opened by jjzieve over 5 years ago

#44 - Release/1.2.0

Pull Request - State: closed - Opened by jjzieve over 5 years ago - 3 comments

#43 - Version 1.2.0

Pull Request - State: closed - Opened by jjzieve over 5 years ago - 1 comment

#43 - Version 1.2.0

Pull Request - State: closed - Opened by jjzieve over 5 years ago - 1 comment

#42 - Precision difference when updating numpy versions

Issue - State: open - Opened by jjzieve over 5 years ago
Labels: bug

#42 - Precision difference when updating numpy versions

Issue - State: open - Opened by jjzieve over 5 years ago
Labels: bug

#41 - Additional fields

Pull Request - State: closed - Opened by jjzieve almost 6 years ago - 9 comments

#41 - Additional fields

Pull Request - State: closed - Opened by jjzieve almost 6 years ago - 9 comments

#40 - Add dockerfile

Pull Request - State: closed - Opened by jjzieve almost 6 years ago - 1 comment

#40 - Add dockerfile

Pull Request - State: closed - Opened by jjzieve almost 6 years ago - 1 comment

#39 - Uses GNU and OSX compatible mktemp

Pull Request - State: closed - Opened by jjzieve almost 6 years ago - 1 comment

#39 - Uses GNU and OSX compatible mktemp

Pull Request - State: closed - Opened by jjzieve almost 6 years ago - 1 comment

#38 - GTC converter - WARNING - Reference is missing entry for chromosomes

Issue - State: open - Opened by cbiOPela almost 6 years ago - 8 comments
Labels: question

#38 - GTC converter - WARNING - Reference is missing entry for chromosomes

Issue - State: open - Opened by cbiOPela almost 6 years ago - 8 comments
Labels: question

#37 - .vcf format for BaseSpace Variant Interpreter?

Issue - State: closed - Opened by cbiOPela almost 6 years ago

#37 - .vcf format for BaseSpace Variant Interpreter?

Issue - State: closed - Opened by cbiOPela almost 6 years ago

#36 - Update download_reference.sh

Pull Request - State: closed - Opened by GvandeSteeg about 6 years ago - 1 comment

#36 - Update download_reference.sh

Pull Request - State: closed - Opened by GvandeSteeg about 6 years ago - 1 comment

#35 - scripts/download_reference.sh fails when missing `realpath`

Issue - State: closed - Opened by GvandeSteeg about 6 years ago

#35 - scripts/download_reference.sh fails when missing `realpath`

Issue - State: closed - Opened by GvandeSteeg about 6 years ago

#34 - Typo in comment on BPMRecord

Pull Request - State: closed - Opened by eyherabh about 6 years ago

#34 - Typo in comment on BPMRecord

Pull Request - State: closed - Opened by eyherabh about 6 years ago

#33 - Possible error in comment on last test

Pull Request - State: closed - Opened by eyherabh about 6 years ago

#32 - About ImportError: No module named vcf.parser

Issue - State: closed - Opened by JeonHyungJin about 6 years ago - 5 comments

#32 - About ImportError: No module named vcf.parser

Issue - State: closed - Opened by JeonHyungJin about 6 years ago - 5 comments

#31 - Few typos and missing punctuation.

Pull Request - State: closed - Opened by eyherabh about 6 years ago

#31 - Few typos and missing punctuation.

Pull Request - State: closed - Opened by eyherabh about 6 years ago

#30 - Python3 compatibility

Pull Request - State: closed - Opened by KelleyRyanM about 6 years ago - 1 comment

#30 - Python3 compatibility

Pull Request - State: closed - Opened by KelleyRyanM about 6 years ago - 1 comment

#29 - Update VcfRecordFactory.py

Pull Request - State: closed - Opened by KelleyRyanM about 6 years ago - 1 comment

#29 - Update VcfRecordFactory.py

Pull Request - State: closed - Opened by KelleyRyanM about 6 years ago - 1 comment

GitHub / illumina/gtctovcf issues and pull requests