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 #70

Closed jma7 closed 6 years ago

jma7 commented 6 years ago

Sorry for post again..

2.1  Import variant info from external files in standard formats (--from_file)

Examples: add genotype info field

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). The error message is 

INFO: Updating variants from V2.vcf (2/3)
ERROR: Specified (SAMP1) and detected sample names (SAMP2) mismatch.

It seems the problem is in https://github.com/vatlab/VariantTools/blob/v3_genoinfo/src/variant_tools/update.py at line 194, will fix later.

jma7 commented 6 years ago 
2.3  Calculate genotype statistics for each variant (--from_stat)

Examples: statistics of genotype info fields

vtools output variant chr pos ref alt DP avg_DP -l5

might need to change to 

vtools output variant chr pos ref alt avg_DP -l5

Since DP is not in the variant table if imported as genoinfo.