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Dear Gatk team,
I have used VariantsToTable to extract specific features, by using the following command:
gatk VariantsToTable -V Annotated_NG.hg19_multianno.vcf -F CHROM -F AF -F MAF -F DP -GF GT -GF AD -GF DP -GF GQ -GF PL -F gnomAD_genome_ALL -F gnomAD_genome_AFR -F gnomAD_genome_AMR -F gnomAD_genome_ASJ -F gnomAD_genome_EAS -F gnomAD_genome_FIN -F gnomAD_genome_NFE -F gnomAD_genome_OTH -O Saudi_NG_gnomAD.txt
And I got the following error:
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 544: unparsable vcf record with allele *TTCT, for input source: Annotated_NG.hg19_multianno.vcf
Could anyone help me in that issue?