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vatlab / vat-docs

Documentation for Variant Tools.
https://vatlab.github.io/vat/
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Documentation: Import #12

Closed BingLi17 closed 6 years ago

BingLi17 commented 6 years ago

Examples: override sample names specified in .vcf file % vtools init import -f % vtools import V*.vcf --build hg18 Maybe change sample name in V2.vcf to SAMP2, sample name in V3.vcf to SAMP3

Import datasets in hg18 and hg19

% vtools init import -f % vtools import vcf/CEU.vcf.gz --build hg18 The second command should be

% vtools import CEU.vcf.gz --build hg18

Skip

2.5  Performance optimization (option --jobs and other techniques) for now.

3.  Importing data in particular formats

Examples: import variant info field DP as genotype info ▸ Putting DP in both var_info and geno_info is confusing and maybe outdated. Consider another example.

Section Performance optimization can be removed. Section on DP in both var_info and geno_info can be removed.

jma7 commented 6 years ago

Error in 

Examples: Using a customized .fmt file to import additional fields
jma7 commented 6 years ago

Fixed.