Closed bf14 closed 8 months ago
Hi Bailey,
I'm sorry to say that I don't work in the field anymore so I won't be able to help you fix this bug. If you manage to debug and fix it by yourself, I would gladly accept a pull request to merge it into the main branch to help others as well!
Hi Paul,
Thank you for your quick response. I will have a go at debugging and let you know if I can get anything to work. I will close this issue for now. Thank you!
Bailey
Hi,
I am attempting to use smart-phase on VCFs from cat and dog tumour samples. However, when I do so, I receive a "contig not in header" error message for both species. After some investigation, I noticed that this error occurs any time smart-phase encounters a non-human chromosome name (e.g. A2 in cat, or 23 in dog). Would you possibly be willing to adapt your code so that it can handle any chromosome name? Any help with this issue would be greatly appreciated. I will put my error messages and their associated files below:
Cat Command:
smart-phase -g CATD0161a_vs_CATD0161b.muts.ids.smartphase.bed -p CATD0161b -r CATD0161b.sample.dupmarked.bam -m0 -x -o CATD0161a_vs_CATD0161b.phased -a CATD0161a_vs_CATD0161b.muts.ids.vcf.gz
Error:
BED file (head):
Dog Command:
smart-phase -g DD1461a_vs_DD1461b.adjacent_snvs.bed -p DD1461b -r DD1461a.sample.dupmarked.bam -m0 -x -o DD1461a_vs_DD1461b.phased -a DD1461a_vs_DD1461b.muts.ids.vcf.gz
Error:
BED file (head):
Many thanks, Bailey