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Created 2012-07-23 23:56:48 | Updated 2012-07-23 23:56:48 | Tags: selectheaders gatkdocs
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Created 2013-10-31 23:25:57 | Updated | Tags: selectheaders gatk
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I would like to know what's the common standards for filtering VCF files? do you filter by depth of coverage or anything else? for exome-sequencing


Created 2013-10-31 18:38:17 | Updated | Tags: selectheaders gatk
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With the vcf output from GATK, I used SelectVariants to select variants with the following conditions:

java -Xmx8g -jar $CLASSPATH/GenomeAnalysisTK.jar \
-T SelectVariants \
-R GATK_ref/hg19.fasta \
-nt 5 \
-V ../GATK/VQSR/parallel_batch/Indels/exome.indels.filtered.vcf \
--excludeNonVariants \
-o ../GATK/VQSR/parallel_batch/Indels/exome.indels.filtered.selected.vcf \
-selectType INDEL \
-select "DP > 30.0"

In the output file exome.indels.filtered.selected.vcf, however, I find some variants have DP < 30, for example:

1/1:0,3:3:12:113,12,0

The bold highlighted 3 is the DP, does this mean SelectVariants did not work on my vcf?