recover unmapped reads
We want to get more information on a variant of interest. We believe we can get more information from recovering unmapped reads . The current whole genome we are looking at is mapped to hg19 reference genome . how can we recover the unmapped reads?
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Adeler001 •
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How to extract unmapped Paired end reads from BWA output sam file
Samtools Unmapped Reads
To extract unmapped pair end reads
By using methods @ATPoint linked above. Assuming your BAM file contains unmapped reads in first place.