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Sambamba is faster at processing SAM/BAM files. In addition, we should provide a streaming example to show the benefits of piping the commands for one single execution to produce BAM.
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I've been using the biodalliance embedded genome browser, but it doesn't support CRAM formatted files, so I was thinking creating a minion web service to wrap a samtools conversion command. Has anyone…
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Looking into the bgzf code I see that it supports reading of totally uncompressed data (eg from zcat foo.bam > bar.bam), apparently due to uncompressed bcf taking this form.
Curious as to how well th…
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**Are you using the latest release?**
If you are not using the latest release of funannotate, please upgrade, if bug persists then report here.
v1.8.13
**Describe the bug**
A clear and concise des…
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We're working on a GPU-accelerated mpileup implementation. We have a generic algorithm working, and now we want to do actual variant calling on the results.
As an intermediate step, we would like t…
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The pipeline hardcodes "samtools sort - " but that usage is deprecated starting with samtools version 1.3. It just prints:
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output fi…
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Hello,
I was wondering if it's possible to add both bam and bed files as input for samtools coverage?
Thanks,
Amy
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Hi,
Thanks for the useful tool. Would it be possible to add the option to modify the headers of the output fastq files? I can see in `aligner.py` that the (final) command for generating clean reads…
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### Description of the bug
gnomAD SV v4.1 (https://gnomad.broadinstitute.org/news/2023-11-v4-structural-variants/) contains some CNVs that don't have AC or AF information in the vcf (gnomad.v4.1.sv.s…
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Hello,
I'm trying to map the reads for each sample to the reference genome,and here is the code:
tophat -p 8 -G ./genome/database/GCA_000187875.1_V1.0_genomic.gtf -o ./quantity/DP_1_thout --no-no…