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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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Error when output variants of samples with genotype value as filter criteria #136

Open mullinyu opened 4 years ago

mullinyu commented 4 years ago

Hi,

I got the error of "Incorrect parameter to function" when I want to output variants of samples with genotype value as filter criteria.

DP_geno is the genotype info and I want to list all the samples of the each variant having DP_geno>24

vtools output variant chr pos ref alt "samples('DP_geno>24')" -l 10 Incorrect parameter to function samples: DP_geno>24

Here's the list of my genotype fields in my database sample_genotype_fields GT,AD_geno,GQ_geno,DP_geno

I"ve read the documentation at http://varianttools.sourceforge.net/Vtools/Genotype but I can't figure it out. I'm not sure if it supports in vtools.

Moreover, I further ran the following and I'm sure there's genotype value associate with samples,

E.g. $vtools output variant chr pos ref alt "genotype('12DG0027')" "genotype('12DG0027', 'field=AD_geno')" "genotype('12DG0027', 'field=GQ_geno')" "genotype('12DG0027', 'field=DP_geno')" -l 10 M 150 T C 2 0,61 99 61 M 195 C A . . . . M 195 C T 2 . 99 52 M 247 G A . . . . M 248 A - 2 . 99 57 M 410 A T 2 1,73 99 74 M 516 - CA . . . . M 516 CA - . . . . M 516 CACA - 2 . 99 179 M 2354 C T 2 1,984 99 985

However, I got error if using genotype() function as follow $vtools output variant chr pos ref alt "genotype('DP_geno>23')" ERROR: Failed to identify a sample using name or condition "DP_geno>23"

Please advise.

Thanks!

Regards, Mullin

BoPeng commented 4 years ago

Are you using the latest variant tools 3.1.1?