search

vatlab / varianttools

software tool for the manipulation, annotation, selection, and analysis of variants in the context of next-gen sequencing analysis
https://vatlab.github.io/vat-docs/
GNU General Public License v3.0
31 stars 4 forks source link

Documentation: Update #69

Closed junma80 closed 6 years ago

junma80 commented 6 years ago 
2.1  Import variant info from external files in standard formats (--from_file)

Examples: import additional fields from source files

It seems there is a bug when run the command 

vtools update variant --from_file V*.vcf --var_info DP NS

in both sqlite and hdf5 version with the updated V2.vcf and V3.vcf files (sample names changed to SAMP2 and SAMP3 respectively). It seems the problem is in https://github.com/vatlab/VariantTools/blob/v3_genoinfo/src/variant_tools/update.py at line 194.