vcf file exported from TASSEL 5.0 GUI don't have information about coverage (depth)

[Arthur Melo]

Hi,

Running TASSEL 5.0 for -mxTagL 64 I produce, after ProductionSNPCallerPluginV2 step, a .h5 file. I open this file in GUI and all things OK. But, I try to export a vcf file with goal to see the depth of SNP calling and using vcftools (vcftools --vcf <vcf_file.vcf> --out <output_file> --depth) to estimate this depth, the result was "-nan". Look:

INDV    N_SITES    MEAN_DEPTH
Male    0    -nan
Female    0    -nan
Female    0    -nan
Female    0    -nan
Male    0    -nan
Female    0    -nan
unknown    0    -nan
Male    0    -nan


Looking (head -20 <vcf_file>) in vcf file, it doesn't have information about depth:

##fileformat=VCFv4.0
##Tassel=<ID=GenotypeTable,Version=5,Description="Reference allele is not known. The major allele was used as reference allele">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the reference and alternate alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
#CHROM    POS    ID    REF    ALT    QUAL    FILTER    INFO    FORMAT    Male   Female    Female    Female    Male    Female  unknown Female
1    70989    S1_70989    C    T    .    PASS    .    GT    1/1    0/0    0/1    0/1    1/1    0/1    0/0    1/1   
1    289370    S1_289370    C    A    .    PASS    .    GT    0/0    0/0    0/1    1/1    ./.    0/0    ./.    1/0
1    344682    S1_344682    G    A    .    PASS    .    GT    1/0    0/1    0/0    0/0    1/0    0/0    0/0    1/0



I would be happy for some help with this issue...

Thank you   

[Lynn Carol Johnson]

HI Arthur -

Depth information was missing in the .h5 file created by ProductionSNPCallerPluginV2.  This has been fixed and will be available in the next TASSEL 5 build.

Max tag lengths > 64 (a previous issue you noted) should also be resolved with the next build.

Thanks - Lynn

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