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[FEATURE] use gVCF with compression #15

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[FEATURE] use gVCF with compression #15

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3 changes: 2 additions & 1 deletion bin/gatk_vc.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,8 @@ OUTPUT_MODE_HC=""
if [[ "$reference_calls" == "True" ]]
then
OUTPUT_MODE_UG="--output_mode emit_all_sites"
OUTPUT_MODE_HC="-ERC BP_RESOLUTION"
# default bands are 5,20,60, we save some space by going 20,60
OUTPUT_MODE_HC="-ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -GQB 20 -GQB 60"
NO_VARIATION="-selecttype no_variation"
fi

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