Eric Boyden

Copied from https://github.com/samtools/samtools/issues/1710 Running samtools 1.19.2 on Linux x86_64 When determining duplicate status or selecting the best representative pair among a pool of duplicates, read pairs should always be considered...

feature request: ubam input/output?

1

Pretty self-explanatory. We are trying to eliminate the need to ever process data in fastq format in our pipeline. We probably wouldn't need the ability to convert fastq to ubam...

feature request: use false positive rate instead of error rate?

2

Hi, I'm a big fan of this software but was wondering if it might make sense to provide the option to threshold based on a false positive rate instead of...

feature request: option to move fastq comments to sam tags

1

Hi, I was wondering if an option to move the fastq comment (everything after the first whitespace, including additional whitespaces) to a field in the output sam file could be...

feature request: option to look for UMI in sam tag

1

Hi, I'm investigating this software as a faster alternative to umi-tools, but our pipeline already extracts UMIs into the `RX` sam tag. Umi-tools can handle this with `--extract-umi-method tag --umi-tag...

bug (?): unexpected results with enforced interval size greater than default

4

When I aligned a pair of fastqs using BWA-MEM2, Bowtie2, or SNAP, and an enforced interval size of 0-500, I got similar results. When I aligned with BWA-MEM2 or Bowtie2...

Is there a means to only print the `LB / PL / PU / SM` tags in the `@RG` header line along with the `ID` tag? As far as I...

feature request: option to mark optical duplicates only

1

Hi - would it be possible to add an option to the duplicate marking function to only mark optical duplicates? Most PCR-free applications, including most WGS workflows, would benefit from...

Duplicate marking produces malformed QS tags in SAM output

3

With `-so` and writing to bam (file or stdout), every read gets a `QS` tag, including duplicates. But when writing to sam (file or stdout), it looks like reads marked...

feature request: ubam support?

11

Pretty self-explanatory. We're trying to eliminate the need to process data in fastq format, so it would be terrific if cutadapt could accept ubam input and write ubam output. (We...