Issue with accuracy

[hlu1992]

I am trying to use xHLA on WES data, however I am not getting the same typing results as with Athlates. I have been previously aligning WES reads to the whole hg38 genome and am about to try aligning to just chr6.

Not doing anything to the BAM file except sorting and indexing after alignment.

bwa mem is run w/out any picard/extra flags

I am running samtools -F 4 flag to remove any unpaired reads though.

[cjieming]

I have similar issue here with accuracy. I ran xHLA on 243 samples from WES data from the 1000 Genomes Project that are also in HapMap, and obtain a massive number of missing calls (~20% for MHC I and 30% for MHC II). The accuracy on the remaining calls is also not high.

Can the authors or somebody comment on how xHLA could be used? Since the paper mentioned an accuracy of 99%, our results seem a bit far from that.

Also perhaps an explanation about the output files would be beneficial for troubleshooting. Thanks!

[abhisheknrl]

Hey guys, I have the same issue. Did you figure if there was something wrong?