The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

#### ☞ Get notifications!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Did you remember to?

1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Did we ask for a bug report?

Then follow instructions in Article#1894.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks (  ) each to make a code block as demonstrated here.

##### Jump to another community
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

# SelectVariants by DP >= 30

DenverMember Posts: 68

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?

Tagged:

## Answers

• Cambridge, MAMember, Administrator, Broadie Posts: 11,651 admin

Hi @rcholic,

I'm not entirely sure this will do it but can you try running again, this time writing the DP cutoff value as an integer (30) instead of a float (30.0). Internally depth should be represented as an integer, and I know JEXL is finicky about types...

Geraldine Van der Auwera, PhD

• DenverMember Posts: 68

thanks Geraldine for reply. With int 30 in the -select still produced something like this "1/1:0,1:1:3:34,3,0". I guess it does not work for me, I will have to use awk to filter it.

• Member, Dev Posts: 544 ✭✭✭✭

I think it's filtering on the DP INFO field (ie, across the entire cohort) rather than the DP FORMAT field which is sample-specific

Sign In or Register to comment.