PharmGKB PharmCAT issues

PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool

Mozilla Public License 2.0

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issues

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VCF preprocessor not working in docker

#97 pjvolders closed 1 year ago
4
How to use Astrolabe's output and pipe it into PharmCAT?

#96 joseph-yclam closed 1 year ago
4
Sort and arrange PGx variants in front of the non-PGx variants at the same genomic positions

#95 BinglanLi closed 2 years ago
0
Preprocessor fails

#94 KarlKeat closed 2 years ago
2
Flag duplicate VCF entries

#93 BinglanLi opened 2 years ago
0
partial and combination allele calls

#92 katrinsangkuhl closed 2 years ago
1
PharmCAT.org website redesign

#91 whaleyr closed 2 years ago
1
java heap space

#90 PWSmit closed 2 years ago
9
Docker running problem

#89 krukanna closed 1 year ago
4
TypeError in vcf preprocess utilities script

#88 jcalendo closed 2 years ago
1
Warnings for non-PGx VCF records

#87 BinglanLi closed 2 years ago
0
Add option for TSV output

#86 whaleyr opened 2 years ago
3
Other formats as outputs for beginners

#85 AngelGarciaDeLaTorreGarcia closed 2 years ago
3
build(deps): bump node-fetch from 2.6.6 to 2.6.7

#84 dependabot[bot] closed 2 years ago
1
Pass warnings and errors from the matcher to report output

#83 whaleyr closed 2 years ago
0
LinkageError?

#82 joseph-yclam closed 2 years ago
1
JNI Error

#81 joseph-yclam closed 2 years ago
1
missing calls - vcf preprocessor issue

#80 PWSmit closed 2 years ago
1
Support for block gVCF

#79 BinglanLi opened 2 years ago
7
Improving Preprocessor's support for phased data

#78 BinglanLi closed 2 years ago
2
Extract pgx regions from input vcf - preprocessing

#77 krukanna closed 2 years ago
1
Allele Definition Preprocessing

#76 CryALotz closed 1 year ago
1
rename sample in the reference pharmcat_position.vcf.bgz

#75 BinglanLi closed 2 years ago
1
build(deps): bump dask from 2021.6.2 to 2021.10.0 in /src/scripts/preprocessor

#74 dependabot[bot] closed 2 years ago
6
Feature to set missing positions to ref

#73 BinglanLi closed 3 years ago
1
Reporter module is missing "-c" option to take in the named allele matcher JSON

#72 BinglanLi closed 3 years ago
2
Retrieve and use bgzip compressed reference human genome fasta for preprocessor

#71 BinglanLi closed 3 years ago
1
Make sure preprocessor normalizes `chrom` field to `chrM` for mitochondria

#70 markwoon closed 3 years ago
1
Make a page with performance metrics

#69 whaleyr opened 3 years ago
0
Change the default output directory

#68 BinglanLi closed 3 years ago
5
This error happens when the `FORMAT` column and the sample column in the VCF do not have the same number of elements.

#67 BinglanLi closed 1 year ago
2
Automatically download positions file from GitHub releases page

#66 BinglanLi closed 3 years ago
0
Fix sorting in positions file

#65 whaleyr closed 3 years ago
2
build(deps): bump semver-regex from 3.1.2 to 3.1.3

#64 dependabot[bot] closed 3 years ago
2
VCF Preprocessor INDELS

#63 pmbock1 closed 3 years ago
3
Issue when running on WGS vcf file

#62 anh151 closed 3 years ago
1
build(deps): bump tar from 6.1.0 to 6.1.11

#61 dependabot[bot] closed 3 years ago
1
Remove all references to "pre-release" right before v1.0 release

#60 whaleyr closed 3 years ago
0
Update disclaimers text

#59 whaleyr closed 3 years ago
4
CNV/Structural variation support

#58 whaleyr opened 3 years ago
0
Missing calls

#57 krukanna closed 3 years ago
8
PharmCAT VCF pre-processing

#56 AlirezaTafazzoli closed 3 years ago
20
build(deps): bump path-parse from 1.0.6 to 1.0.7

#55 dependabot[bot] closed 2 years ago
1
Compiling project to jar

#54 jkaefer closed 3 years ago
5
build(deps): bump tar from 6.1.0 to 6.1.5

#53 dependabot[bot] closed 3 years ago
1
build(deps): bump trim-newlines from 3.0.0 to 3.0.1

#52 dependabot[bot] closed 3 years ago
2
build(deps): bump normalize-url from 5.3.0 to 5.3.1

#51 dependabot[bot] closed 3 years ago
2
How can I run the analog tool to astrolabe and Stargazer?

#50 Philips-omica-io closed 3 years ago
1
could i use my 23andme data to apply this assay?

#49 Philips-omica-io closed 3 years ago
3
how process data imputed to determinate the haplotype?

#48 Philips-omica-io closed 3 years ago
3

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