Hi
When i run vt used vcf with all the chr, it would stop but no err log. So i split the genome through chr and run vt separately. However,only one chr is successful which in vcf is first.
When i use "vt normalize 3.sort.diploid.vcf.gz -n -w 1000000 -r",it had erro "[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: GWHCAYC00000003:87941-87942". But i had checked the all the file,chr_name is GWHCAYC00000003. Other all chr is so, but i don't know how to correct it. I only use one reference genome.
Thanks,
Xoey
Hi
When i run vt used vcf with all the chr, it would stop but no err log. So i split the genome through chr and run vt separately. However,only one chr is successful which in vcf is first.
When i use "vt normalize 3.sort.diploid.vcf.gz -n -w 1000000 -r",it had erro "[variant_manip.cpp:67 is_ref_consistent] failure to extract base from fasta file: GWHCAYC00000003:87941-87942". But i had checked the all the file,chr_name is GWHCAYC00000003. Other all chr is so, but i don't know how to correct it. I only use one reference genome.
Thanks,
Xoey