The major issue of The WES data from patient derived xenofraft samples (i.e, human tissue that is engrafted in mouse) is mouse contamination. This program removes mouse reads and ambiguous reads from the aligned BAM files. This program was written for the BAM files aligned with BWA-MEM.
The program take three arguments: mouseAlignment humanAlignment outputPrefix
The program has 10 stats outputs and four BAM file outputs: ( WES FAStq file is a paired end reads)
Stats output:
Human_only reads = Aligned perfectly to human reference
Human_better reads = Both the pair has better score for human alignment
Human_better_one reads = one of the pair has better score for human alignment
Human_better_mixedreads = Difference in pair score favouring human alignment
Mouse_only reads= Aligned perfectly to mouse reference
Mouse_better reads= Both the pair has better score for mouse alignment
Mouse_better_one reads= one of the pair has better score for mouse alignment
Mouse_better_mixed reads=Difference in pair score favouring mouse alignment
Mixed reads = Scores are mixed in pairs cannot decide
Tie reads = scores are tied.
BAM output:
Human only reads , Humanonly+Human better reads , Humanonly+Human better+Humanbetterone reads and mouse reads
Program acknowledgement : Timothy Mosbruger : [email protected]