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BaseRecalibrator only doing recalibrations on substitutions, not indels

Hello, I am trying out BaseRecalibrator. My command is:

gatk BaseRecalibrator \
      --reference reference.fa \
      --input input.bam \
      --known-sites good_filtered_snps.vcf \
      --known-sites good_filtered_indels.vcf \
      --output recal_table

The output recalibration table only include information for substitutions (event type "M"), none for insertions or deletions, which other people's recalibration tables seem to have. I cannot find anything in the BaseRecalibrator help or in its output that explains why I'm only getting a third of the recalibration table.


Best Answer


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