Post-alignment analysis

Once a SAM/BAM has been generated, a number of post-processing steps can be undertaken.

Detecting chimeras

Coverage smoothing

Further contamination removal

Counting and removing duplicates

Realignment around indels

Removing reads with indels

`SamRemoveIndels https://github.com/centre-for-virus-research/VATK/blob/master/AssemblyPostProcessing/SamRemoveIndels.awk`_ is an awk script which is used in the HCMV pipeline to remove reads with indels from a SAM file.

` SamRemoveIndels samfile.sam > samfile_with_without_indels.sam `

Remove the duplicate fragments

`UniqSamPE https://github.com/centre-for-virus-research/VATK/blob/master/AssemblyPostProcessing/UniqSamPE.awk`_ is awk script to remove duplicate paired-end fragments that start and end at the exact same position. This script is used in the HCMV pipeline to measure the level of clonality in a given alignment, i.e, it remove reads lacking unique fragment coordinates.

` UniqSamPE.awk samfile.sam > samfile_with_unique_reads.sam `