-
## Bug Report
### Affected tool(s)
_MarkDuplicates_
### Affected version(s)
- [x] Latest public release version [version?]
- [ ] Latest development/master branch as of [date of test?]
### …
-
Hi, I want to report a potentially problematic behaviour using pysam.fetch on AWS S3 bucket infrastructure. Using the following pseudo code on a Bam file in a S3 Bucket will create requests without a …
-
Similar to #11 I'd like to make my decoil ecDNA calls more conservative. But most of my samples have ~25-30x and I don't want to downsample them and loose information unnecessarily.
With default…
-
While merging the original `@PG` headers now works great, it looks like there is no PP: tag added. Ex.:
```
$ samtools view -H 12MapBWA/BASE__r03_F000__01.bam | grep "^@PG"
@PG ID:bwa PN:bwa VN:0…
-
Hi @CS-GustaveRoussy any suggestions on how to convert usual vcf (https://samtools.github.io/hts-specs/VCFv4.2.pdf) to ICGC-like vcf?
thanks in advance
-S
-
What Bam format is needed to input in groopm? I have tried a couple different BAM conversions and sorting with samtools (see BAM generation), I get errors about the BAM files (error output below for g…
-
**Snakemake version**
8.20.5
**Describe the bug**
When using a fresh Conda environment with Mamba and Snakemake as currently provided by Conda-forge and bioconda, the `--use-conda` option to …
-
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 …
-
Hi,
I'm running bis-snp when using the command:
java -Xmx10G -jar BisSNP-1.0.1.jar -R hs37d5.fa -I header.sort.mdups.bam -D 00-All.vcf.gz -T BisulfiteGenotyper -vfn1 header.sort.mdups.cytosine.raw.v…
-
**Are you using the latest release?**
v1.8.15
**Describe the bug**
I am new to this and am having a hard time understanding the differences between --species, --busco_seed_species, and --august…