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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
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--from_stat VTOOLS v 2.7.0 #11

Open BoPeng opened 7 years ago

BoPeng commented 7 years ago

I have 49 individuals in one sample but actually, using --from_stat to define the number of WT genotype for example I obtain numbers like 98.. My sample is well define.

When I use:

vtools update variant --from_stat 'N_heterozygalt=#(het)' --samples "pheno='0'" -j8

Vtools INFO is: INFO: 49 samples are selected which is the correct number of individuals but, when I do an output, I have:

chr   ref   alt   #(wtGT)  #(het)  #(hom) #(alt)
1        T       A             4       24      70      164

but I have only 49 individuals..

When I used vtools v2.6.2 I did not have this issue.

BoPeng commented 7 years ago

Could you send me the exact command for your do an output? It would be best if you could send me, even in private email, a sample vcf file and commands to reproduce the problem. Thanks.