Hi, Can anyone tell me that how to filter primary alignment from the bam file. i have paired end data and mapped the data on genome using bwa. Now, i want to filter reads that have primary alignment from bam file because i want to identify SNPs and its important that i should remove secondary align reads from the bam file. i searched for the answer but do not get satisfactory answer. So please anyone can tell me that how to get reads from bam.
Thanks & Regards Deepika