In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
Hi,
I am trying to genotype my samples using Seq2HLA, but the results indicate all my samples are homozygous in all of the 3 MHC-I genes. Here is the output from one of the samples.
Hi, I am trying to genotype my samples using Seq2HLA, but the results indicate all my samples are homozygous in all of the 3 MHC-I genes. Here is the output from one of the samples.
Command: python $script/seq2HLA.py -2 BWA_reads_50M_AlleleSet10_1.fastq -1 BWA_reads_50M_AlleleSet10_2.fastq -r AlleleSet10_Seq2HLA
HLAgenotype2digits file:
Locus Allele 1 Confidence Allele 2 Confidence
A A16 0.3422678 hoz("A10") 8.00000000023e-07 B B02 0 hoz("B02") NA C C044 0.7426947 hoz("C011") 0.0056835
HLAgenotype4digits file:
Locus Allele 1 Confidence Allele 2 Confidence
A A16:01 0.3422678 A16:01 8.00000000023e-07 B B02:3 0.0 B02:3 NA C C044:01 0.7426947 C044:01 0.0056835
I am thinking maybe I didn't use it correctly. Do you notice anything wrong in my command?
Thanks, Yuan