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GATK220.127.116.11 failed to call an validated variant
There is an variant showed as the uploaded
For this alt allele , 43 reads supported this site , with 18 on + strand , 25 on - strand .
This variant has been validated and it exists in this bam file, but it cannot be called to use GATK4 !!!.
So what's wrong with this tool ? It's a bug of GATK4 ?
The command I use as the below, hope it's useful ! :
~/gatk-18.104.22.168/gatk Mutect2 \
-R $fasta \
--read-validation-stringency SILENT \
-I $tumor_bam \
Expecting your answer !
Thanks in adavance !