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### Description of the issue:
When reading a VCF with HTSJDK it causes an exception when there is a duplicate ALT allele.
I believe duplicate ALT alleles are allowed in VCF, and are used in cases wh…
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Hello,
I posted on issue #392 to try to reopen it since the problem remains in `minimap2` `v2.26`, but the issue remains closed, so I'm opening a new issue.
Here's what we're seeing:
I doubt …
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bed.gz files are sometimes incompletely loaded when accessing them from google cloud.
It's unclear what set of conditions causes this to happen, but it seems to be deterministic and repeatable.
…
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We could benefit from downloading and formatting SRA accessions provided as input, to normalize also public available data. Exploring the SRA handling from htsjdk will help to improve it.
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Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 147517, Read name HWI-EAS324_96694046:7:77:833:7#0, bin field of BAM record does not equal value comp…
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Hello,
I have RNASeq data (tumor and normal samples) and I'm using your pipeline to detect somatic variants. However, I encountered the following error while running the pipeline. Your assistance w…
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I've got a number of `0/0, 0/0, 0/0` reported in a VCF file so I will need to do some filtering.
I've never used `vcffilter` before and the manual isn't very clear for some parameters:
```
--de…
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Hi,
I try to view a bam file but it generates an error. I just provide the reference which seems valid and the bam file, not other annotations.
ASCIIGenome -fa ../ref/2A.fa ../bamsource/2A/16NAS…
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Hi @bwlang
I ran the following command : pilon --genome assembly.fasta --bam C8_sorted.bam --threads 40
its giving this error:
Pilon version 1.24 Thu Jan 28 13:00:45 2021 -0500
Exception in t…
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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 …