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VariantsToTable question
estif74
Saint Paul, MN, USAMember ✭
Hi there,
When using the VariantsToTable function, is there a way to force the genotypes to be numeric, i.e. 0/1 or 0/0 rather than the actual bases like G/T, G/G, etc.? I can't seem to find anything in the tool documentation, but maybe there's another way.
Thanks,
Steve
Tagged:
Best Answer

Sheila Broad Institute ✭✭✭✭✭
@estif74
Hi Steve,Unfortunately, there is no option to do that. Please have a look at this thread: http://gatkforums.broadinstitute.org/discussion/4801/genotypesandvariantstotablewalker
Sheila
Answers
@estif74
Hi Steve,
Unfortunately, there is no option to do that. Please have a look at this thread: http://gatkforums.broadinstitute.org/discussion/4801/genotypesandvariantstotablewalker
Sheila
If you are working with only biallelic sites you can use
F HET F HOMVAR
to get the GT information in a more usable form, then use (dirty) tricks like the following:Thanks! That's helpful :) I was able to use some potentially less dirty tricks in Excel to get this working given that my (current) dataset is somewhat manageable in size.
To get a genotypes table with 0, 1 and 2 representing genotypes, I used Plink to generate a binary dosage format. https://www.coggenomics.org/plink2/data
Abracadabra ...
Hi,
I can't figure out why the FT field is being represented as NA instead of PASS or lowGQ. Can someone explain this? thanks.
T VariantsToTable \
R /work/lianglab/bin/GATK/resources/hg19/ucsc.hg19.fasta \
V /work/lianglab/wgs/ASD/VCF/GATK/GATK.chr1.recalibratedVariants.filtered.vcf \
SMA \
F CHROM \
F POS \
F ID \
F REF \
F ALT \
GF GT \
GF FT \
o /work/lianglab/wgs/ASD/VCF/GATK/GATK_chr1_C1_results.table \
RESULTS:
chr1 10146 rs375931351 AC A AC/AC NA ./. NA AC/AC NA AC/AC NA AC/AC NA AC/AC NA AC/AC NA AC/AC NA ./. NA AC/AC NA ./. NA ./. NA AC/AC NA ./. NA ./. NA ./. NA ./. NA AC/AC NA ./. NA ./. NA AC/AC NA AC/AC NA ./. NA AC/AC NA ./. NA ./. NA AC/AC NA AC/AC NA AC/AC NA ./. NA ./. NA ./. NA ./. NA ./. NA AC/AC NA ./. NA AC/AC NA AC/AC NA ./. NA AC/AC NA ./. NA AC/AC NA AC/AC NA AC/AC NA AC/AC NA ./. NA AC/AC NA ./. NA AC/AC NA AC/AC NA ./. NA ./. NA AC/AC NA ./. NA AC/AC NA ./. NA ./. NA ./. NA AC/AC NA AC/AC NA ./. NA ./. NA ./. NA ./. NA ./. NA AC/AC NA ./. NA ./. NA ./. NA AC/AC NA ./. NA AC/AC NA AC/AC NA AC/AC NA ./. NA ./. NA ./. NA AC/AC NA ./. NA AC/AC NA AC/AC NA AC/AC NA ./. NA AC/AC NA ./. NA AC/AC NA ./. NA AC/AC NA AC/AC NA AC/AC NA ./. NA AC/AC NA ./. NA AC/AC NA AC/AC NA ./. NA ./. NA