what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
Entering edit mode
17 months ago
dare_devil ★ 1.6k

I am converting vct to table using following command:

gatk VariantsToTable -V my_input.vcf -F CHROM -F POS -F ID -F REF -F ALT -F QUAL -F FILTER -F AC -F AF -F AN -F DP -F ExcessHet -F FS -F MLEAC -F MLEAF -F MQ -F QD -F SOR -F CSQ -GF GT -GF AD -GF DP -GF GQ -GF PL -O my_input.table

But, I want to split multi-allelic and put them into table. The gatk forum says about using -SMA option with ASF & ASGF option to perform the function. To what all parameter I should add ASF &ASGF option.

As far I know, need to put for AF, AC, DP, GT, AD, DP, GQ

variantstotable gatk vcf picard • 426 views

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