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Check OSTEP - 2.5 Design goals
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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 a…
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Hi, thank you for developing this and making it available. I have some VDJ seq data I'm hoping to use this on, but I can't seem to figure out where I'm going wrong with it. It seems like I'm able to g…
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Is there any way to obtain the quality (r2 or INFO) of imputing HLA-* ?
So far, after doing the prediction I can only see the alleles and only one probability.
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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 paired tumor and normal WES or RNA…
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Specifying either --hla_table or --hla results in error: "Unknown option". Documentation isn't clear on which is correct, and --help doesn't list it in the options. This is a really exciting feature a…
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Email Martin B with the list of patient identifiers and the data elements we want for the NHIC export
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When i use hla_scan on WGS data.sometimes i get wrong :ERROR: wrong HLA gene
i use :
hla_scan –b [Bam file] –v 38 –d dir_to_db/db –t 8
no matter i add -g or not ,it still wrong.
sometime it go …
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Hi there,
I would like to kindly inquire, if I input a BAM file that is aligned to 'GRCh38_full_analysis_set_plus_decoy_hla.fa', when executing 'ERVcaller_v1.4.pl', should the '-H' parameter inpu…
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When launching the AAMS run:
`python aams_pipeline.py -M ../output/runs/test_run/run_tables/test_pair_test_run_mismatches_20_400_5_gq_20_0.8_bl_3.tsv -T ../output/runs/test_run/run_tables/test_pair_t…