Hi Melanie,
Thanks for developing such amazing tool!
I encountered a problem when I want to view the vcf file using IGV or JBrowse, where we have to zip and index the vcf file prior to viewing. I tried indexing the merged vcf file using tabix and have this error:
[E::hts_idx_push] Chromosome blocks not continuous
tbx_index_build failed: JASMINE_OUTPUT.vcf.gz
And when I try to view the vcf file using bcftools view multiple lines of these errors were shown:
[E::vcf_parse_format] Incorrect number of FORMAT fields at NC_041754.1:10646142
[E::vcf_parse_format] Incorrect number of FORMAT fields at NC_041754.1:17253351
[E::vcf_parse_format] Incorrect number of FORMAT fields at NC_041754.1:18671051
Can you point out something I have done wrong? I have a feeling this is not a JASMINE problem, but a format issue. I tried sorting the individual sample vcf files before running JASMINE, and still the same problem persist. Many thanks in advance for your help!
Hi Melanie, Thanks for developing such amazing tool!
I encountered a problem when I want to view the vcf file using IGV or JBrowse, where we have to zip and index the vcf file prior to viewing. I tried indexing the merged vcf file using
tabix
and have this error:And when I try to view the vcf file using
bcftools view
multiple lines of these errors were shown:I ran JASMINE using the following script:
Can you point out something I have done wrong? I have a feeling this is not a JASMINE problem, but a format issue. I tried sorting the individual sample vcf files before running JASMINE, and still the same problem persist. Many thanks in advance for your help!
Best, Rifa