VariantsToTable in GATK does not produce the table of all SNPs in the vcf file

Question

[Ana]

I am trying to convert my vcf file to a flat tab-separated format by using "VariantsToTable" in GATK. I am particularly interested in DP at the sample annotation for my analysis. I am using

/data/programs/gatk-4.0.4.0/gatk VariantsToTable -V final.vcf -GF DP -O snps.DP.tab

My vcf file consists of over 4 million SNPs, but the table that I get from running VariantsToTable consists only nearly 1 million SNPs. I wonder what is wrong! Does anyone knows how can I sort this out. Thanks

[finswimmer]

Hello,

were there any warning/error messages? Could you post some examples from the vcf file from variants that are missing in the result?

Thanks.

fin swimmer

[Ana]

No, I did not get any error message. I just get only 1 million SNPs in the table and I do not know which of them from the main vcf file

[snehakoneru]

I have the same question. I am using VariantsToTable command and it removes all the lowQual SNPs. However, I want them too. for example,

chrI    1873123 .       G       A       0       LowQual AC=0;AF=0.00;AN=2;DP=34;Dels=0.00;ExcessHet=3.0103;FS=0.000;HaplotypeScore=0.0000;MLEAC=0;MLEAF=0.00;MQ=54.32;MQ0=0;SOR=0.412   GT:AD:DP:GQ:PL  0/0:34,0:34:99:0,99,1262

The following command works

gatk-4.beta.5/gatk-launch VariantsToTable -R ce10.fa -V Galaxy19-VCFcombine__on_data_18_and_data_17.vcf -F CHROM -F POS -F REF -F ALT -GF AD -GF DP -GF GQ -GF PL -O bothbulks_new.table

but not the following command

gatk-4.beta.5/gatk-launch VariantsToTable -R ce10.fa -V Galaxy19-VCFcombine__on_data_18_and_data_17.vcf -F CHROM -F POS -F REF -F ALT -GF AD -GF DP -GF GQ -GF PL -noTrim TRUE -O bothbulks_new.table

Thank you, Sneha

Answer 1

[Christopher Walker]

This is answered in the description of the tool on the Broad's website:

"By default, the tool only extracts PASS or . (unfiltered) variants in the VCF file. Filtered variants may be included in the output by adding the --show-filtered flag"

Answer 2

[BunnyBosZ]

FYI:: https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable#--show-filtered