biobambam2
biobambam2 copied to clipboard
gt1
Tools for early stage alignment file processing
Hi, I am new to using this tool (2.0.69) but find it weird why commandline arguments are not systematically shared or why some apllications lack arguments supposedly common to your...
If after clipping the sequence in a bam file has a single base with a quality of 9, which corresponds to a '*' in the sam format, bamclipreinsert doesn't restore...
Hi, I'm running biobambam2 on a high cpu/RAM host and have been attempting to improve the throughput by modifying various parameters but I'm not having much luck. I'm assuming that...
Is there any way it would be possible to use multiple cores in this stage? Is 1 to decompress BAM, 1 to process, and 1 to compress per output file...
German; We're using bamcat/bamsormadup within bcbio to merge 27 input BAMs with: ``` bamcat level=0 `cat files.txt` | bamsormadup threads=8 ``` We expect a ~130Gb output file from the merge....
Hi, This is a great tool (I mostly use bamsormadup), but would it be possible to all for parameters to specify an input and output file? Thank you, Mark
Would it be possible to add the ability to split a BAM by the readgroups durring the collate phase similar to the way that `bamtofastq` does? ``` outputperreadgroup= : split...