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Hi,
I have a problem in understanding samtools fixmate and rmdup.
I have paired-end whole exome data. I filtered for properly paired reads that map uniquely, which resulted in equal amounts of reads with bitwise flag 99 and 147 as well as 83 and 163. Next I tried to remove PCR duplicates with rmdup. In the resulting sam file the number of reads with 99 differs from that with flag 147, and the same for 83 and 163. Isn't it the case that always BOTH of the mates are PCR duplicates?
So I tried to first run fixmate. But fixmate seems to change the flags, because suddenly I had reads with flags 73,89,137 and 153. Why does this happen?
Do I need to run fixmate before rmdup?
Thanks!
I have a problem in understanding samtools fixmate and rmdup.
I have paired-end whole exome data. I filtered for properly paired reads that map uniquely, which resulted in equal amounts of reads with bitwise flag 99 and 147 as well as 83 and 163. Next I tried to remove PCR duplicates with rmdup. In the resulting sam file the number of reads with 99 differs from that with flag 147, and the same for 83 and 163. Isn't it the case that always BOTH of the mates are PCR duplicates?
So I tried to first run fixmate. But fixmate seems to change the flags, because suddenly I had reads with flags 73,89,137 and 153. Why does this happen?
Do I need to run fixmate before rmdup?
Thanks!