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When trying to annotate with Haplogrep2, it complains because INFO contains whitespace from gnomAD. Source gnomAD VCF already contains this, so I need to fix it at the Dockerfile.
Exception is as …
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First proposal, taking the last commont of @tfenne in https://github.com/samtools/htsjdk/issues/896:
* `htsjdk-core`: common code, interface/api definitions for things and then the implementations…
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Hi, I'm working with long chromosomes (barley) that require .csi indexing instead of .bai. Is this currently supported in gridss?
The specific error that I'm getting is:
```
ERROR 2022-10-14 15:2…
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Finally got bamstats04 to work, but at one point I get this error:
htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 9505, Read name HWI-D00104:87:D1GYYACXX:5:1112:13918:71031, …
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I tried the method you mentioned solve the problem if the input is cram format, but still reported an error.
Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/commons/compress/…
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We can add a travis test to run every week/month on the later htsjdk/gatk master branch to keep our dependencies up-to-date and see if there are putative errors arising from update the dependencies.
…
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I created a subset file with seven samples out of two thousand and saved it to disk. IGV won't open it.
> htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line n…
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Issue seems to due to VM running out of disk space. From a MergeVCF log:
```
[Thu Jun 25 08:23:53 UTC 2020] picard.vcf.MergeVcfs done. Elapsed time: 89.52 minutes.
Runtime.totalMemory()=202729062…
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**Hello, it is great work.**
**However, I encontered error in the very first step following your tutorial.**
**The script I was using is shown below:**
java -Xmx20G -cp "target/FinaleMe-0.…
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Hello, thanks for the plugin!
I am having some issues with it, though. It is apparently deleting intermediate files marked for use in upcoming processes. When running my pipeline (which I created m…