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 on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
from gatk calling multiplesamples vcf to plink
Hi GATK team,
This is maybe a bit of a stupid question and I might not get the concept of calling samples at the same time. Anyway when I use this command for GATK for my 5 rnaseq samples to call SNPs:
java -jar /home//Desktop/variant_calling_rnaseq/GATK/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar \ -R /media/Data/HG19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa \ -T HaplotypeCaller \ -I split1.bam -I split2.bam -I split3.bam -I split4.bam -I split5.bam\ -o region_of_interest.vcf \ --dbsnp /media/Data/HG19/Homo_sapiens/UCSC/hg19/Annotation/dbsnp141/new_all_141.vcf \ -L chr1:30000000-38000000 \ -stand_call_conf 50.0 \ -stand_emit_conf 10.0 \ -U ALLOW_N_CIGAR_READS
then I want to convert the vcf file to a plink file to continue analysis, then only one sample is present, while the input into GATK was 5 files:
$ vcftools --vcf region_of_interest.vcf --plink --out plink_file VCFtools - v0.1.7 (C) Adam Auton 2009 Parameters as interpreted: --vcf region_of_interest.vcf --out plink_file --plink VCF index is older than VCF file. Will regenerate. Building new index file. Scanning Chromosome: chr1 Writing Index file. File contains 46 entries and 1 individuals. Applying Required Filters. After filtering, kept 1 out of 1 Individuals After filtering, kept 46 out of a possible 46 Sites Writing PLINK PED file ... Writing PLINK MAP file ... Done. Run Time = 0.00 seconds
Hope you can clarify this for me