[Useq-users] samtools mpileup error for data aligned with novoAlign and Useq

[nimrod r. <ru...@po...>]

Hi,
I have RNA-seq data that I've aligned using novoAlign to mm10 knownGene
indexed with Useq, and converted transcriptomic coordinates to genomic
coordinates with Useq as well. Trying to call variants with samtools
mpileup then crashes for some of the libraries I have, with this error
message:
[bcf_sync] incorrect number of fields (6 != 5) at 15:62640916.

I was wondering if this may have anything to do with Useq and if so how can
that be fixed.

Thanks,
rubi