TonyKess

> @rizkg @droazen I just saw this issue was still open, and I was curious if this problem was addressed in the May release (1.3.0) of DRAGMAP or if you...

Same message unfortunately. This is using the joint-germline workflow with a species without any prior genomic info (indels, dbSNP etc). The joint-germline.vcf itself actually seems fine, but seems like vcftools...

quick update: disabling vcftools seems to lead to pipeline completion

I'm going to try to use some high depth samples to build a SNP/indel reference, and will see if including that info in subsequent runs changes the performance here.

Thanks for this advice! We are checking out BLAS now, and looking into building some checks on internal stats for when we are using really large datasets. We've used RDA...

Thanks! Most of this data is unpublished and not shareable yet, so any instructions on building indexes would be great! For the VCF index, are individual reference genotypes needed, or...