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
`