Hello, Thanks for the tool.
I'm not familiar with HLA typing.
Instead of using ExtractHLAread.sh, I exact HLA by directly align reads towards HLA ref sequences like this:
But the output is empty.
Could you give me some advise? thanks !
Start profiling HLA for HLA.
use 4 threads.
WARNING: 1396881 reads are detected, please check if they are HLA-related reads. If not, please extract HLA-related reads first. Otherwise, the process will be slow.
WARNING: 1362932 reads are detected, please check if they are HLA-related reads. If not, please extract HLA-related reads first. Otherwise, the process will be slow.
map the reads to database to assign reads to corresponding genes.
Detect novoalign license, use novoalign.
start assigning reads...
read bam cost 0.0010614395141601562
read no. for A is 0.
read no. for B is 0.
read no. for C is 0.
read no. for DPA1 is 0.
read no. for DPB1 is 0.
read no. for DQA1 is 0.
read no. for DQB1 is 0.
read no. for DRB1 is 0.
read assigment cost 153.634530544281
start realignment...
Attention: please ensure the platform can run gzip -l automatically, otherwise, it may not continue.
BAM and VCF are ready.
Mean depth {'HLA_A': 0, 'HLA_B': 0, 'HLA_C': 0, 'HLA_DPA1': 0, 'HLA_DPB1': 0, 'HLA_DQA1': 0, 'HLA_DQB1': 0, 'HLA_DRB1': 0}
Minimum Minor Allele Frequency is 0.05.
Num of hete small variant is 0 in HLA_A.
No heterozygous locus, no need to phase.
seg [1001, 4503, 'normal', '.']
Phasing of HLA_A is done!
Num of hete small variant is 0 in HLA_B.
No heterozygous locus, no need to phase.
seg [1001, 5081, 'normal', '.']
Phasing of HLA_B is done!
Num of hete small variant is 0 in HLA_C.
No heterozygous locus, no need to phase.
seg [1001, 5304, 'normal', '.']
Phasing of HLA_C is done!
Num of hete small variant is 0 in HLA_DPA1.
No heterozygous locus, no need to phase.
seg [1001, 10775, 'normal', '.']
Phasing of HLA_DPA1 is done!
Num of hete small variant is 0 in HLA_DPB1.
No heterozygous locus, no need to phase.
seg [1001, 12468, 'normal', '.']
Phasing of HLA_DPB1 is done!
Num of hete small variant is 0 in HLA_DQA1.
No heterozygous locus, no need to phase.
seg [1001, 7492, 'normal', '.']
Phasing of HLA_DQA1 is done!
Num of hete small variant is 0 in HLA_DQB1.
No heterozygous locus, no need to phase.
seg [1001, 8480, 'normal', '.']
Phasing of HLA_DQB1 is done!
Num of hete small variant is 0 in HLA_DRB1.
No heterozygous locus, no need to phase.
seg [1001, 12229, 'normal', '.']
Phasing of HLA_DRB1 is done!
start annotation...
parameter: sample:HLA dir:SpecHLA/HLA pop:Asian wxs:whole G_nom:0
Start G group resolution annotation...
The region with low read depth is masked by N. The cutoff is specified by -k.
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_A.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_A.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_B.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_B.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_C.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_C.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_DPA1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_DPA1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_DPB1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_DPB1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_DQA1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_DQA1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_DQB1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_DQB1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.1.HLA_DRB1.fasta
The ratio of N (masked) is 1.0 for the allele SpecHLA/HLA/hla.allele.2.HLA_DRB1.fasta
Clean output dir.
# version: IPD-IMGT/HLA 3.38.0
Sample HLA_A_1 HLA_A_2 HLA_B_1 HLA_B_2 HLA_C_1 HLA_C_2 HLA_DPA1_1 HLA_DPA1_2 HLA_DPB1_1 HLA_DPB1_2 HLA_DQA1_1 HLA_DQA1_2 HLA_DQB1_1 HLA_DQB1_2 HLA_DRB1_1 HLA_DRB1_2
HLA - - - - - - - - - - - - -
HLA is done.
Hello, Thanks for the tool.
I'm not familiar with HLA typing.
Instead of using
ExtractHLAread.sh, I exact HLA by directly align reads towards HLA ref sequences like this:This would resoult in a much larger
bamfile with much more reads.But the output is empty.
Could you give me some advise? thanks !
std output: