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Tags:
  • genomics
  • Working with the cloud

    export GCS_OAUTH_TOKEN=$(gcloud auth application-default print-access-token)

    Interval notes

    • samtools view -L <bed> does not use the index, but rather iterates over all reads start-to-finish. You need to explicitly specify samtools view -ML.

    • Samtools (and GATK) interval subsetting includes all reads that overlap the interval. This is sometimes not desired behavior, since it makes it difficult to create scatter intervals that are disjoint with respect to reads they contain.

      As such, piping the output of samtools view to a simple helper tool is necessary.