HLA identification

[obricard]

Hello,

I would like to identify the HLA alleles of some samples sequenced with Solid (50bp single end). My first idea was to extract a sam file containing the reads mapped in HLA locus (using samtools) then convert it in fastq (using picard) and finally use seq2HLA. The problem is that seq2HLA need paired end read. I saw that HLAminer could also do the job. The problem is that I can manage to type a correct command line : I tried : perl HLAminer.pl -a myfile.sam ; but it get this :
Usage: HLAminer.pl [v1.0.5]
Derivation of HLA class I and II predictions from Shotgun sequence datasets
--------------------------------------------------------------------
HPTASR (HLA Predictions by Targeted Assembly of Shotgun Reads):
-b blastn alignments.........................<tig_vs_hla-ncbi.coord>
-r reciprocal blastn.........................<hla_vs_tig-ncbi.coord>
-c contig fasta file.........................<TASRhla200.contigs>
-z minimum contig size.......................<200>
------------------------------- OR ---------------------------------
HPRA (HLA Predictions by Read Alignment):
-a sam alignments............................<ngs_vs_hla.sam>
--------------------------------------------------------------------
-h hla fasta file............................<HLA_ABC_CDS.fasta>
-p P-designation file........................<hla_nom_p.txt>
-i minimum % sequence identity...............<99>
-q minimum log10 (phred-like) expect value...<30>
-s minimum score.............................<1000>
-n consider null alleles (1=yes/0=no)........<0>
-l label (run name) -optional-

Could you help me ?

Thanks in advance

[rwarren]

you have to specify the hla reference sequence file (-h) at a minimum..

-h hla fasta file............................<HLA_ABC_CDS.fasta>