-
BRAKER3 worked for several genomes, but did not for a genome. As shown below, the error occurred as described in the title.
```
singularity exec -B /ddn:/ddn /app/centos8/braker/braker-20230308/br…
-
Dear @brentp
Recently, I tried to use smoove to detect CNV using the BAM file generated by BWA-MEM as input. However, lumpy_filter always gave me an error: "Segmentation fault (core dumped)"; thus…
-
`test/vcf/4.3/passed/complexfile_passed_000.vcf` has an invalid unstructured header line:
https://github.com/samtools/hts-specs/blob/401e2ec3e8ecf19fa89def74e9c27c1e40df341e/test/vcf/4.3/passed/com…
-
The current samtools view behavior is to extract any read that overlaps with the target region, I wonder if it is possible to add an option to select only reads whose start coordinates fall inside the…
-
## Bug Report
### Affected tool(s)
_picard ValidateSameFile_
### Affected version(s)
- [x] Latest public release version [3.1.1]
- [ ] Latest development/master branch (not tested)
### Des…
-
Hi,
I have this error that seemed to be coming from freebayes, I have googled but still have no idea of how to solve it.
### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-c…
-
Dear author,
I am trying to merge SVs detected from assemblies and reads.
Here is one call from assemblies:
Here is another call from reads:
The merge command is:
```
Jasmine fi…
-
Hi, Dr. Song
I successfully generated alignment.maf using AnchorWave and converted it into a BAM file using the provided script. However, when I attempted to convert the BAM file to a VCF file using …
-
I wonder if it is possible to use pipe as input to bismark_methylation_extractor instead of file? something like
samtools view bam.bam|head -1| bismark_methylation_extractor
jksr updated
8 months ago
-
Hi,
We still need "wbu" mode for pipe output, such as
bwa | samtools fixmate | samtools sort
but now 'samtools view -u ' is changed from 'wbu' to 'wb0', and the 'wbu' support in the sou…