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Thread | Thread Starter | Forum | Replies | Last Post |
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#1 |
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Location: Italia Join Date: Jul 2012
Posts: 27
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Dear all,
has somebody attempted HLA typing with bwakit and can share some experience? I have whole exome sequencing data of human individuals for who I would like to do HLA typing. I ran the bwakit as instructed in the Readme, but have problems interpreting the output. Here are the first few lines from the out.hla.all for HLA-B for one individual. Code:
HLA-B*50:01:01 HLA-B*55:01:01 0 0 2 HLA-B*50:01:02 HLA-B*55:01:01 0 0 2 HLA-B*50:01:04 HLA-B*55:01:01 0 0 2 HLA-B*50:01:01 HLA-B*55:01:03 0 0 2 HLA-B*50:01:02 HLA-B*55:01:03 0 0 2 HLA-B*50:01:04 HLA-B*55:01:03 0 0 2 HLA-B*50:01:01 HLA-B*55:01:07 0 0 2 HLA-B*50:01:02 HLA-B*55:01:07 0 0 2 HLA-B*50:01:04 HLA-B*55:01:07 0 0 2 column 3: #mismatches on the primary exon(s) column 4: #mismatches on all considered exons column 5: #exons used in typing My questions are: 1. What are columns 1 and 2? I would have expected results for one allele, not two. 2. What is the "best" or the "true" allele? The out.hla.top file simply gives the first line of the out.hla.all for each gene, but from the evidence in the out.hla.all file, the first line does not seem to be better than the second or third. 3. Would you say that given high coverage exome sequencing data, one should be able to clearly identify (with bwakit) the true allele an individual has for each of the HLA genes? Thank you Eva Last edited by evakoe; 05-08-2017 at 06:08 AM. |
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#2 |
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Location: Italia Join Date: Jul 2012
Posts: 27
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For the people interested in this post:
1. I assume the first two columns are the HLA alleles for the two human alleles, so the HLA-B allele is heterozygous in this case. 2. The coverage was probably not high enough to determine a six digit resolution. After all, the first four digits are allthe same, and the last two are variable. I ran OptiType on the same sample which gave the output Code:
B1 B2 B*50:01 B*55:01 Last edited by evakoe; 05-17-2017 at 02:51 AM. |
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#3 |
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Location: Heidelberg Join Date: Jun 2010
Posts: 14
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hi evakoe,
which command did you use? cuz i'm trying to do the same but it's not working. i'm using this: run-bwamem -o NA12878-hs38 -t 20 -H -s /gpfs/data_jrnas1/ref_data/Hsapiens/hs38DH/hs38DH.fa NA12878_2.fastq.gz NA12878_1.fastq.gz |sh and it doesn't give me sorted bam or HLA typing. |
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#4 |
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Location: Italia Join Date: Jul 2012
Posts: 27
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The command I used was
Code:
run-bwamem -t 4 -R "@RG\tID:myID\tSM:mySM\tPL:myPL\tLB:myLB\tPU:myPU" -H -d -s -o sample BWAindex sample_1.fastq sample_2.fastq | sh |
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Tags |
bwakit, hla, hla typing, typing |
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