warrenlr
commented
3 years ago hello, thanks for your message and interest in HLAminer.
Predictions only appear in the csv file if they meet the minimum thresholds:
prompt> ./HLAminer.pl
Usage: ./HLAminer.pl [v1.4]
-i minimum % sequence identity...............<99>
-q minimum log10 (phred-like) expect value...<30>
-s minimum score.............................<1000>The log will track everything. You may wish to lower the above thresholds to see predictions in the csv, but at the risk of a lower confidence in predictions.
Lastly, know that WES isn't the typical use-case for HLAminer, as certain HLA alleles may not be picked up by exon capture probes.
good luck!
kwanghoon821
Hi, I used HLAminer for the first time using WES data generated from FFPE sample.
Can you check my command and results?
This is for alignment bwa mem -t 20 -M path/to/database_bwamem/HLA-I_II_CDS.fasta A_1.fastq.gz A_2.fastq.gz > HLAminer_A.sam
This is for typing path/to/HLAminer.pl -a HLAminer_A.sam \ -h path/to/database_bwamem/HLA-I_II_CDS.fasta \ -p path/to/database/hla_nom_p.txt \ -l A_result
And this is results in csv file. No result for HLA-A,B,C,E
HLA-F Prediction #1 - F01 | | F01:01:03:01 | 2413.96 | 7.78E-17 | 161.1 F*01:01P | 1614.99 | 1.82E-11 | 107.4
HLA-G Prediction #1 - G01 | G01:01P | 1614 | 2.56E-14 | 135.9 G*01:04P | 1008 | 3.20E-09 | 84.9
Log file has results of HLA-A,B,C,E. Should I see log file?
Thank you!