Hi all,
I am running picard MarkDuplicates with REMOVE_DUPLICATES=TRUE.
From what I have read, if picard marks a primary alignment as a duplicate, its secondary alignments should also be marked as a duplicate (and removed). However, I seem to be left with secondary hits after running the above command. For example, when looking at one example read (below), the original file has one primary alignment and one secondary alignment
Original file
-bash-4.2$ grep "1101:14851:94564" Sample006_CA.sam
HWI-ST614:206:C63DHACXX:7:1101:14851:94564 0 MT 16503 60 67M33S * 0 0 GGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCAC
HWI-ST614:206:C63DHACXX:7:1101:14851:94564 256 MT 1 60 67H33M * 0 0 GATCACAGGTCTATCACCCTATTAACCACTCAC
(Duplicates removed)
-bash-4.2$ grep "1101:14851:94564" Sample006_rd.sam (after running picard MarkDuplicates)
HWI-ST614:206:C63DHACXX:7:1101:14851:94564 256 MT 1 60 67H33M * 0 0 GATCACAGGTCTATCACCCTATTAACCACTCAC
Can anyone help explain why I am left with secondary alignments? This becomes an issue when running the gatk BQSR as it screens out secondary alignments.
Thank you in advance,
Hannah
I am running picard MarkDuplicates with REMOVE_DUPLICATES=TRUE.
From what I have read, if picard marks a primary alignment as a duplicate, its secondary alignments should also be marked as a duplicate (and removed). However, I seem to be left with secondary hits after running the above command. For example, when looking at one example read (below), the original file has one primary alignment and one secondary alignment
Original file
-bash-4.2$ grep "1101:14851:94564" Sample006_CA.sam
HWI-ST614:206:C63DHACXX:7:1101:14851:94564 0 MT 16503 60 67M33S * 0 0 GGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCAC
HWI-ST614:206:C63DHACXX:7:1101:14851:94564 256 MT 1 60 67H33M * 0 0 GATCACAGGTCTATCACCCTATTAACCACTCAC
(Duplicates removed)
-bash-4.2$ grep "1101:14851:94564" Sample006_rd.sam (after running picard MarkDuplicates)
HWI-ST614:206:C63DHACXX:7:1101:14851:94564 256 MT 1 60 67H33M * 0 0 GATCACAGGTCTATCACCCTATTAACCACTCAC
Can anyone help explain why I am left with secondary alignments? This becomes an issue when running the gatk BQSR as it screens out secondary alignments.
Thank you in advance,
Hannah
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