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The bamout file results are inconsistent with the VCF file results

houruihourui ChinaMember
Hi,

I use GATK4 were analyzed, and found that took place on a site of "bamout" file multiple mutations, respectively from G mutation is T, the number of reads supported mutation is 14, and from G mutation into C, the number of reads supported mutation is 11, but in the "ALT" column in the VCF file just is T, and "GT = 0/1", I'm sure the original bam had been removed duplicate reads, and the reads supported the two variable are higher quality.

This question confuses me, why does the VCF file only give one variation?

Can you help me? Thank you very much! :)

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