Hi,
I have results of whole exome NGS (SureSelect, enrichment by hybridization) as fastq files and I want to get the the list of target sequences that are not covered by at least x reads (for example, 10 reads).
Do anyone know how to do that?
Even if there is a software that can give me for each base in the target bases how many reads cover it (consensus+variant) - it will be excellent.
I have the list of targets as positions (i.e. chrn:1234568-4564567)
I can do alignment with BWA, MAQ, etc.
I will be gratefull for any hint!
Lilach
I have results of whole exome NGS (SureSelect, enrichment by hybridization) as fastq files and I want to get the the list of target sequences that are not covered by at least x reads (for example, 10 reads).
Do anyone know how to do that?
Even if there is a software that can give me for each base in the target bases how many reads cover it (consensus+variant) - it will be excellent.
I have the list of targets as positions (i.e. chrn:1234568-4564567)
I can do alignment with BWA, MAQ, etc.
I will be gratefull for any hint!
Lilach
Comment