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.

Got a problem?


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 2.10.4 has MAJOR CHANGES that impact throughput of pipelines. Default compression is now 1 instead of 5, and Picard now handles compressed data with the Intel Deflator/Inflator instead of JDK.
GATK version 4.beta.2 (i.e. the second beta release) is out. See the GATK4 BETA page for download and details.

best way of filtering out common SNPs in the GATK outputted VCF file

In my PiCard/GATK pipeline, I already include the 1000G_gold_standard and dbsnp files in my VQSR step, I am wondering if I should further filter the final vcf files. The two files I use are Mills_and_1000G_gold_standard.indels.hg19.vcf and dbsnp_137.hg19.vcf, downloaded from the GATK resource bundle.

I recently came across the NHLBI exome seq data http://evs.gs.washington.edu/EVS/#tabs-7, and the more complete 1000G variants ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/

These made me wonder if I should use these available VCFs to further filter my VCF files to remove the common SNPs. If so, can I use the "--mask" parameter in VariantFiltration of GATK to do the filtration? Examples below copied from documentation page:

    java -Xmx2g -jar GenomeAnalysisTK.jar \
       -R ref.fasta \
       -T VariantFiltration \
       -o output.vcf \
       --variant input.vcf \
       --filterExpression "AB < 0.2 || MQ0 > 50" \
       --filterName "Nov09filters" \
       --mask mask.vcf \
       --maskName InDel
Tagged:
Sign In or Register to comment.