We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Should I provide the exome target list (-L argu) even while calling gVCF file using Haplotypecaller?
Recently we performed exome sequencing using Nextera Illumina platform for three samples (Father, Mother and Son). I downloaded the exome interval list from Illumina's website.
1) Trimmed the raw reads
2) Aligned the trimmed reads against the human reference hg19 as recommended for exome-sequencing
3) Then sorted, deduped, recalibrated the bam file.
4) Then performed variant calling in two steps process for all three samples individually
4.1) Used the GATK Haplotype Caller tool in GVCF mode
Command: java -Xmx16g -jar GenomeAnalysisTK.jar - T Haplotypecaller -R /GATK_bundle/hg19.fa -I sample1.sorted.dedup.recal.bam --emitRefConfidence GVCF --dbsnp /GATK_bundle/dbsnp.138.hg19.vcf -o sample1.raw.g.vcf
4.2) Used GenotypeGVCFs (Joint SNP calling) for all three samples together
Command: java -Xmx16g -jar GenomeAnalysisTK.jar - T GenotypeGVCFs -R /GATK_bundle/hg19.fa --variant sample1.raw.g.vcf --variant sample2.raw.g.vcf --variant sample3.raw.g.vcf --dbsnp /GATK_bundle/dbsnp.138.hg19.vcf -o sample1.2.3.trio.raw.vcf
In the above command, I didn't use the Illumina's exome interval list used for targeting the exomes in sequencing process.
As per this link "https://software.broadinstitute.org/gatk/documentation/article.php?id=4669", under the example section of GATK command lines, for exome sequencing the article suggests us to provide the exome targets using -L argument.
I have following queries,as per the aforementioned article
1) Should I provide the exome target list (-L argument) only while calling regular VCF file using Haplotype caller?
2) Should I provide the exome target list (-L argument) even while calling gVCF file using Haplotype caller?