HATK

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HLA2PED conversion call from HATK.py not working: workaround

2

First of all: Thank you for the author for made HATK available. Documenting a workaround so it may help other users. The command referenced on the link below is not...

steletvinicius

imgt2seq error at DRB1 in IMGTHLA3480

2

Hi there, I am trying to integrate a newer version of the IMGT Database for my analysis but there seems to be an issue at the DRB1 locus. I downloaded...

anjatietz

I am using the following code, slightly modified from the example code, and getting the below error ` python HATK.py \ --hg 18 \ --hped example/wtccc_filtered_58C_RA.hatk.300+300.hped2 \ --bfile example/wtccc_filtered_58C_RA.hatk.300+300.hg18.chr6.29-34mb \...

zoequandt

alicekiki

Errno 2 in Association test

2

I am running complete analysis using hg38, but get the following error. Your suggestion will be very useful .... ... [9] Making reference panel for HLA-AA, SNPS,HLA, and Normal variants...

dineshpeace

No output from HATK.py --hla2hped

2

Hi Wanson, I found you again here. I have generated HIBAG files and ran --hla2hped without any output; what went wrong? My data looks like these, ==> hla-A.txt hla-B.txt hla-C.txt...

jinghuazhao

Hi, I wonder if there is any efficient way to covert SNP2HLA dosage file to HPED that can be fed into your downstream analysis pipeline? Thanks

xiw588

Just wondering if there is a quick way to convert HLA-TAPAS (SNP2HLA, in VCF) output to HPED format? Thanks!

psytky03

Association output only on SNPs

4

Hi there, When I run HATK on one dataset, the association output has only worked for SNPs with rsids. The following error is displayed and no heatmaps are produced? Do...

ciaran-campbell

Cannot find gcc/gxx version 7.3.0

1

I had an issue where conda had an issue finding the appropriate gcc and gxx versions. On closer analysis on the conda repository, I found that some of the packages...

juliandwillett