Question: VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
1
gravatar for Ana
12 months ago by
Ana170
Ana170 wrote:

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

gatk • 810 views
ADD COMMENTlink modified 3 months ago by snehakoneru0 • written 12 months ago by Ana170

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

ADD REPLYlink written 12 months ago by finswimmer12k

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

ADD REPLYlink written 12 months ago by Ana170

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

ADD REPLYlink modified 3 months ago by RamRS23k • written 3 months ago by snehakoneru0
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