smoove paste error for DEL

[olivia-gc]

Hi Brent! I am experiencing the following command error using smoove paste (directly after processing through smoove genotype):

Command error:
[smoove] 2024/06/26 01:33:55 starting with version 0.2.6
[smoove] 2024/06/26 01:33:55 squaring 9 files to DEL.smoove.square.vcf.gz
[smoove] 2024/06/26 01:34:54 all files had 127089 variants
[smoove] 2024/06/26 01:35:04 The REF prefixes differ: GTTACCTACCGCTGCGACCAGTTGATTACTGAGTGG vs GTTACCTACCGCTGCGACCAGTTGATTACTGAGTGG  (56,56)
[smoove] 2024/06/26 01:35:04 Failed to merge alleles at chr9:132825235 in DEL.sample1-smoove.genotyped.vcf.gz
  2024/06/26 01:35:05 exit status 255

Do you have any ideas on how to solve this error or where it comes from? Thank you!

[brentp]

hi, smoove paste is a thin wrapper over bcftools merge. I think you'll have to have a look at that variant in all files and make sure the REF alleles match. You could either remove that variant manually, or edit the ref allele.