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```
If you set outSAMattributes as All then the sam file generated is incompatible
with Cufflinks. The error is something like no XS tag for a spliced read. But
when one uses outSAMattributes in st…
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### Community Note
* Please vote on this issue by adding a 👍 [reaction](https://blog.github.com/2016-03-10-add-reactions-to-pull-requests-issues-and-comments/) to the original issue to help the…
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```
What steps will reproduce the problem?
1. bamToBed -i foo.bam -split
on the following foo.bam file
@HD VN:1.4 GO:none SO:coordinate
@SQ SN:chr9 LN:124076172
@RG ID:sample1 P…
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When I create a new bam record, the new bam record seems to truncate the read name at 23 characters. I am using the following code (note that this is part of a larger program; I just stopped it in th…
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**Version:** Buyer-Dev-Version-1.0.2
**Devices:** All
**Repro Steps:**
1. Advance to Checkout Summary.(Official YiLinker Product With Super Ultra...)
2. User voucher (350f1144 -9999.99) or (2adb1109 …
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Dear hts-specs maintainers,
First, thank you for all the great work! Second, I ran into a problem when using one of the vcf examples as a test file. I am currently working on [the biowdl scatter to…
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**Describe the bug**
It seems that the MD tag generated in Chromap sometimes can incorrectly begin with a letter. It seems this behavior, to my understanding occurs when the first character is a 0. Mo…
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(A) Convert FASTQ to uBAM and add read group information using FastqToSam
Picard's FastqToSam transforms a FASTQ file to an unmapped BAM, requires two read group fields and makes optional specificati…
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Dear Alaina,
I've been trying to set up the latest version of liftoff in a MacBook (M1) and a linux-based HPC following all your instructions. Both conda and pip liftoff installation fail.
### c…
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It would be good if desktop IGV could render features in a GFF file in specified colors depending on the feature type. It would also be good if a feature label could be directly visible on the featur…