Hlacaller Gatk

Question

[GouthamAtla]

I have been trying to use HLA Caller, as a first step to analyse HLA data.

This tool is no more developed and not supported.

I could run the pipeline but ending up with no results as the input files ( intervals, frequencies, dictionary ) etc have a different corrdinate system compared to the build I am using( hg19 ). I would like to know if any one knows which build to use to align the data to use GATK HLACaller pipeline ?

Or if any one has any alternate solutions to deal with the HLA data other than GATK pipeline . My data is ROCHE 454, C-DNA amplicon sequencing.

Thanks in advance.

Answer 1

[favero.francesco]

I've tried seq2HLA with illumina RNA-seq and, after some minor corrections on the code, it did work quite well.

It gives you a resolution only on 2 digits though (eg HLA-A02). For this you need fastq files, that will be aligned to various HLA reference sequences with bowtie. I don't know if this is the ideal setup for 454 though.

[GouthamAtla]

seq2HLA works only with paired-end data like illumina.