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.
Here Heng Li explains the meaning of columns 3 to 5:
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
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
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