no calls gives unusual file sets

[keiranmraine]

If CaVEMan gives no calls during the estep you get a full set of *.muts.vcf files but no *.snps.vcf.

This causes the mergeCavemanResults script to fail.

Not sure how this should be handled ot classified as the data is of no use but a clean run with a warning would be helpful. I encountered this when running an WXS pair from cghub where it appears the tumour and normals don't have any common coverage.

[ghost]

Unless CaVEMan silently failed between opening and writing the header to the muts file and doing the same for the snps fil I can't see how this could be possible. Is it still replicatable?

[ghost]

I'll test this and attempt to replicate it soon using an empty normal bam.