Tagged with #selectheaders
1 documentation article | 0 announcements | 2 forum discussions


Comments (0)

A new tool has been released!

Check out the documentation at SelectHeaders.

No posts found with the requested search criteria.
Comments (1)

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

Comments (4)

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?