SpecHLA

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Question about minimap2 parameters in long_read_typing.py

15

Hi! I'm running long_read_typing.py for PacBio -reads for which I have extracted the HLA-regions (originally aligned data to chm13, then extracted hla with HLA*LA and ran bam2fastq). I was wondering...

karoliinas

Feature request

7

Would it be possible to add an option to specify the HLA database folder to use, rather than using the hardcoded 'db' option?

Redmar-van-den-Berg

Identify somatic HLA mutation from SpecHLA

6

Hi, Thank you for developing this tool which is quite easy to use! I am wondering if SpecHLA could also be used to detect somatic HLA mutations since we have...

LongpanUPC

ExtractHLAread.sh

5

Hi, When I apply the ExtractHLAread.sh script, the unpaired reads produced are far more than the paired reads. After researching, I saw that some people say the bam file should...

vegetableyu

Novoalign

1

Hi there, do you have a plan to replace commercial Novoalign with a non-commercial aligner? This publication (https://link.springer.com/article/10.1007/s00521-021-06188-z) compared 17 aligners where the SEGEMEHL seems to be a competitive one....

bsb2014

DRB3 and DRB5

15

Hi, can SpecHLA type DRB3 and DRB5 as kourami? Thanks

bsb2014

what's the meanning of "interval_dict" in long_read_typing.py ?

5

Hello , professor, For "A":"HLA_A:1000-4503" from the below code line , what's the meaning for these two number "1000" and "4503" ? and how to get these coordinate number values...

lidd77

how to get hla_gen.format.filter.extend.DRB.no26789.fasta ?

3

Hello, could you tell us how to get this ref file , hla_gen.format.filter.extend.DRB.no26789.fasta ? I checked this fasta , for example , it is only 2-field fasta sequence . so...

lidd77

Followed the readme step by step but got error with example data

1

Hi, I am trying to run "test_whole.sh" with example data "whole". but it gives the following error at "phase_variants.py" step. I lack novoalign lic so the script use bowtie2 instead....

Fang-Kevin

Hello, When I updated IMGT version to 3.5x , for same samples , I find some gene's allele typing result changed . such this situtation is normal ? which result...

lidd77