variant calling: dict and indexing

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Nagarajan Raju

• February 05, 2023 14:23

Hi,

For variant calling suing Haplotypecaller, I created dict and indexing for the reference genome. Should I create index files for the input genome (bam) file also? Also, should I sort the bam file before variant calling (link for commands please)?

Thanks

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  Louis Bergelson

  • February 06, 2023 17:55

  Hi Nagarajan Raju,

  You do need to sort the bam file and indexing it after sorting.  If you haven't done the other preprocessing steps we recommend you might want to do those as well (MarkDuplicates, BQSR).

  There is an article describing our recommended steps.  The sorting happens usually as part of the MarkDuplicates step using the tool called SortSam.

  The simplest example would be something like this:

  gatk SortSam INPUT unsorted.bam OUTPUT sorted.bam SORT_ORDER coordinate

   

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