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 October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
GATK reports wrong allele
I downloaded the following BAM file: ftp://ftp.sra.ebi.ac.uk/vol1/ERA596/ERA596386/bam/Burkhardtshohle.bam
I sorted and indexed the file with samtools.
Then I created a VCF with the following command:
java -Xmx4g -jar GenomeAnalysisTK.jar -l INFO -R resources/Homo_sapiens_assembly19.fasta -T UnifiedGenotyper -I Burkhardtshohle_sorted.bam -L Y -rf BadCigar -o Burkhardtshohle.vcf --output_mode EMIT_ALL_SITES -nct 4
At position Y:7190277 it reports reference allele A and no alt allele. However, the BAM file has G at this position. I also ran this with HaplotypeCaller and similar options but it still gave me A instead of G.
Am I doing something wrong, or...?