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bioinformatics Basic Samtools

Count number of records per reference in bamfile

samtools idxstats thing.bam

Convert sam into bam (and back again)

Samtools can be used to convert between sam and bam:

  • -b indicates that the input file will be in BAM format
  • -S indicates that the stdout should be in SAM format
samtools view -sB thing.bam > thing.sam

And to convert between sam and bam:

samtools view thing.sam > thing.bam
samtools sort thing.bam thing
samtools index thing.bam

This will produce a sorted, indexed bam. This will create the files thing.bam and thing.bam.bai. To use a bam you must have an index file.

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