seq2HLA HLA typing from RNA-Seq sequence reads

Release: 2.2

seq2HLA is an in-silico method, written in python and R, which 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

Inputs

Paired read fastq files with illumina style IDs.

Outputs

1. <prefix>-ClassI.HLAgenotype2digits => 2 digit result of Class I
2. <prefix>-ClassII.HLAgenotype2digits => 2 digit result of Class II
3. <prefix>-ClassI.HLAgenotype4digits => 4 digit result of Class I
4. <prefix>-ClassII.HLAgenotype4digits => 4 digit result of Class II
5. <prefix>.ambiguity => reports typing ambuigities (more than one solution for an allele possible)
6. <prefix>-ClassI.expression => expression of Class I alleles
7. <prefix>-ClassII.expression => expression of Class II alleles

ClassI.HLAgenotype4digits

#Locus	Allele 1	Confidence	Allele 2	Confidence
A	A*03:01	0.000510333	A*02:01'	0.0005975604
B	B*50:01	0.001271273	B*58:02	3.52561e-05
C	C*04:01	0.06362723	C*06:02	0.04725865

ClassI.expression

#Locus	RPKM
A	89.59
B	139.66
C	184.42