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vatlab / vat-docs

Documentation for Variant Tools.
https://vatlab.github.io/vat/
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Documentation: Update #9

Closed BingLi17 closed 6 years ago

BingLi17 commented 6 years ago 
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.

 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.