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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...?