no ref calls after squaring

[brentp]

I'm running:

bcbio-variation-recall merge -c $threads eiee.2.vcf.gz $ref 15-00229*.vcf.gz
bcbio-variation-recall square -r 2:1-243199373 -c $threads -m freebayes eiee.2.square.vcf.gz $ref eiee.2.vcf.gz file.list

I don't see any error messages. When I look at eiee.2.square.vcf.gz there are no reference calls, but the program ran without errors. Any ideas?

As an unrelated FYI, I noticed that if I run without -r or with -r 2, then it errors.

[brentp]

I'm just trying again now by putting eiee.2.square.vcf.gz into file.list. I'm guessing it's not using any bams in file.list when I invoke as above

[chapmanb]

Brent -- sorry about the issues. Do the sample names in the BAM files match those in the VCF inputs? That's the most likely cause of failing to square these. It does need to have a region specified. Apologies, it's not that smart with parallelization and is mostly meant to get driven from bcbio. Hope the BAM/VCF resolution fixes the problems.