I'm trying the following strategy to remove duplicates from small subsets of interest:
samtools view -b test.bam chr1:7660315-7660315 | samtools rmdup - - | samtools view -
...but it doesn't seem to remove anything. Am I doing something wrong syntactically, or do I perhaps have some of that data that rmdup doesn't work on? How do I tell if I have FR orientation, or if ISIZE is correctly set? (I'm new to using BAMs, and I don't create them myself.)
Here's a sample line.
938_1080_925 16 chr1 590592 0 30M * 0 0 TCATGTCAACTGCAAACAGAAACAATTTAA :BIIIICIIIIIIIIIHIIIIIIIIIIIII RG:Z:0 CS:Z:T003003011002211001312101211312 CQ:Z:?0>59;7=/;=><54<5<39?/@/5>3A):
(And yes, according to other posts, "I should really use Picard for this". But that has weird Java problems on my system that I don't have the time or permissions to fix.)
Thanks!
samtools view -b test.bam chr1:7660315-7660315 | samtools rmdup - - | samtools view -
...but it doesn't seem to remove anything. Am I doing something wrong syntactically, or do I perhaps have some of that data that rmdup doesn't work on? How do I tell if I have FR orientation, or if ISIZE is correctly set? (I'm new to using BAMs, and I don't create them myself.)
Here's a sample line.
938_1080_925 16 chr1 590592 0 30M * 0 0 TCATGTCAACTGCAAACAGAAACAATTTAA :BIIIICIIIIIIIIIHIIIIIIIIIIIII RG:Z:0 CS:Z:T003003011002211001312101211312 CQ:Z:?0>59;7=/;=><54<5<39?/@/5>3A):
(And yes, according to other posts, "I should really use Picard for this". But that has weird Java problems on my system that I don't have the time or permissions to fix.)
Thanks!
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