Problem with indexing merged vcf file

[athenasyarifa]

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

I ran JASMINE using the following script:

jasmine file_list=vcf_ALL_FILES.txt out_file=JASMINE_OUTPUT.vcf out_dir=/path/to/JASMINE/OUTDIR

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

[Mannyari]

Hi Rifa,

I have exactly the same problem and could not find any solution. Did you?

Many thanks,
Arianna