VariantsToTable GT not extracting correctly

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Asha Mehta

• October 15, 2021 19:59
• Edited

Why do I see the GT field not being extracted correctly when I run:

java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /oak/stanford/groups/euan/tools/gatk/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar VariantsToTable -V {input_vcf} -F CHROM -F POS -F END -F SVTYPE -GF GT -O {output_table}

Instead of printing the genotype in the output .table file, it prints a part of the sequence. 

The GT field is listed in the header as part of the FORMAT field and I am able to filter on GT with bcftools:

bcftools filter -i 'FORMAT/GT=="1/1"' {input_vcf}

The VariantsToTable command does work successfully for me with a vcf generated by the Dragen pipeline but not for a vcf that was generated with the Manta pipeline. What might be causing this difference? 

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  Pamela Bretscher

  • October 22, 2021 14:37

  Hi Asha Mehta,

  Can you clarify what you mean by "prints a part of the sequence"? The GATK team doesn't support Manta, so I wouldn't know how the generates the GT field, but I would assume that there is simply a difference in the algorithms that is resulting in a different value being printed for different tools. 

  Kind regards,

  Pamela

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