kourami

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Hello, I wanted to start using Kourami in one of my projects. And am wondering if this is still being maintained. Thanks, Rashesh

Rashesh7

When using IMGT/HLA 3.53.0, calling Kourami.jar to genotype an extracted bam will result in an NPE in MergeMSFs.java. This was traced to HLA*26:236 being present in hla_nom_g.txt but absent in...

dhuen

Duplicate reads in BAM

2

Hi, This tool is very useful in my workflow but I have a question about the preprocessing step. The chr6 coordinates overlap causing the final alignment to have duplicate primary...

JenniferShelton

I am running Kourami on several samples and ran into the following error with just one sample: ``` java.lang.IndexOutOfBoundsException: Index: 0, Size: 0 at java.util.ArrayList.rangeCheck(ArrayList.java:659) at java.util.ArrayList.get(ArrayList.java:435) at HLAGraph.pathAlign(HLAGraph.java:1296) at...

anoronh4

I used kourami with IMGTHLA version: 3.49.0 (the latest update from https://github.com/ANHIG/IMGTHLA/). I run with four options of HGV favor: hs38,hs38D,hs38DH,hs38NoAltDH. However, all outputs are empty and logs are the...

mainguyenanhvu

DRB5_gen wrong with IMGT/HLA Release 3.40.0 and HLA Release 3.41.0

1

Hi i have try HLA Release 3.40.0 and HLA Release 3.41.0,they all go wrong with DRB5. And i noticed that Release 3.40.0 and HLA Release 3.41.0 noly have DRB_nuc.txt,but with...

masen1991

Hello, I was wondering if you have any suggestions on what cutoff to use for the bottleneck weights. Most of the values from my data fall within the range of...

Rashesh7

java.lang.NullPointerException during Bubble Processing

9

Hi, I'm was running Kourami on a dozens of samples and for a few of them, I get this java error: ``` Bubble Processing and Path Assembly for: A Bubble...

ariane-lozachmeur

formatIMGT.sh NullPointerException

10

Hi again, I have downloaded the Alignments_Rel_3330.zip from https://github.com/ANHIG/IMGTHLA and put the hla_nom_g.txt in that folder. It seem to be working fine at first to create the new reference with...

zezzipa

typing additional loci

19

hi, when i use the -a option it only types A,B,C,DQA1,DRB1. if i specify -a MICA for instance, i get the message "Input bam : A DOES NOT exist. Please...

afadda91