I input my original bam file (which have the whole genome mapped reads) to arcasHLA and input chr6-splited bam file to optitype for genotyping. I notice that arcasHLA first splits the chr6 bam and then goes for the rest. So the input of arcasHLA and optitype should be the same.
But when I got genotyping results, I found they are largely different.
I'll paste one of my sample results as an example:
From arcasHLA:
Sample1: HLA-A\*24:361, HLA-A\*24:361,HLA-B\*59:10N, HLA-B\*59:01:01,HLA-C\*01:185Q, HLA-C\*01:185Q
From Optitype:
Sample1: A*02:06 A*24:02 B*51:01 B*59:01 C*01:02 C*14:02
I'm not very familiar with programming and HLA genotyping. I'm not sure what cause these differences. Any suggestions?
BTW, should the first four number extracted from 6-digit genotype equals the 4-digit genotye for the same patient?
I input my original bam file (which have the whole genome mapped reads) to arcasHLA and input chr6-splited bam file to optitype for genotyping. I notice that arcasHLA first splits the chr6 bam and then goes for the rest. So the input of arcasHLA and optitype should be the same.
But when I got genotyping results, I found they are largely different.
I'll paste one of my sample results as an example:
From arcasHLA:
Sample1: HLA-A\*24:361, HLA-A\*24:361,HLA-B\*59:10N, HLA-B\*59:01:01,HLA-C\*01:185Q, HLA-C\*01:185QFrom Optitype:
Sample1: A*02:06 A*24:02 B*51:01 B*59:01 C*01:02 C*14:02I'm not very familiar with programming and HLA genotyping. I'm not sure what cause these differences. Any suggestions?
BTW, should the first four number extracted from 6-digit genotype equals the 4-digit genotye for the same patient?
Thank you.