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andreas-wilm / lofreq3

LoFreq Version 3
MIT License
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gatk indel qualities #16

Closed jeongmeani closed 4 years ago

jeongmeani commented 4 years ago

Hi,

using lofreq, i analysis WES data to discover variant.

but the indel output vcf does not any indel. so i check manual again, i realize indel qualities is required for indel calling.

but my bam file is carried out to BQSR. and i could not search any information about indel qualities of BQSR.

so i want to check 'indel qualities' how can i?

Best Regards

Jeongmin

andreas-wilm commented 4 years ago

Hi Jeongmin, I think GATK recently stopped adding indel qualities (BI and BD tags) to the BAM during BQSR. You can add those with lofreq indel (best with --dindel).