SplitNCigarReads output bai file

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Tamar Lahav

• January 19, 2020 09:11

Can you please provide
a) GATK version used

4.1.4.1
b) Exact GATK commands used

../../../tools/GATK/gatk-4.1.4.1/gatk SplitNCigarReads -R ../reference_genome/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa -I name.Aligned.sortedByCoord.RG2.bam -O name.Aligned.sortedByCoord.RG2.splite.bam

c) The entire error log if applicable.

No error, but I don't understand why it creates a bai file (together with bam file). I don't care, it is good for me but want to understand if it is the right way to do it.

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  Anton Kovalsky

  • January 22, 2020 17:47

  Hi Tamar Lahav, thanks for your question!
  
  The BAI file is the index for the BAM that allows for querying different positions, so both are necessary when you want to subset your data. GATK tools that take a BAM input usually also require the BAI as an input. 

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