what are the parameters we should change when we run VariantsToTable of GATK in splitting multi allelic mode?
0
0
Entering edit mode
8 months ago
dare_devil ★ 1.5k

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 • 228 views
ADD COMMENT

Login before adding your answer.

Traffic: 2518 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6