sambamba

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samsonjm

Hi, I have a problem with sambamba depth region. sambamba version: 0.6.6 Command: sambamba depth region -t 8 -L units.bed sorted_Pooled_cis.bam output: #. chrom chromStart chromEnd F3 F4 readCount meanCoverage...

QichenFU

I try: sambamba depth region -L $bed $sample1.bam $sample2.bam ... > output.bed and I expected to get multiple coverage columns that indicate the multiple input bams in one output, but...

yuanjianwen-gif

Why does `sambamba sort` give me a different sort order across multiple runs (on the same BAM file)? Isn't `sort` by coordinates determinstic?

2

Running `sambamba sort` on the same BAM `input.bam` file gives me differing results from one run to another. Is this expected behavior? I'm not sure what's causing this but the...

etrh

Feature request: fixmate like samtools

1

after bwa mem, the samtools suggested fixmate/sort command before mark duplicates. Is any way to implement those by sambamba now or add fixmate in sambamba in future? Thanks!

kaji331

Feature request: Slice BAM file by query name

1

Wish sambamba can help quickly pick out alignment records based on query name list. Like samtools view -N after version 1.12. Much appreciated.

yangyxt

Dear developer, thanks a lot for this fast tool, can sambamba calculating ngs data duprate

asmlgkj

sambamba --version's output doubled

1

``` $ sambamba --version sambamba 0.8.2 by Artem Tarasov and Pjotr Prins (C) 2012-2021 LDC 1.27.1 / DMD v2.097.2 / LLVM11.0.0 / bootstrap LDC - the LLVM D compiler (1.27.1)...

kim-fehl

`Samtools + libdeflate` out performs `sambamba` on a single thread

3

Hello, I recently heard about `sambamba` and it's performance gains over `samtools`, and was excited to compare it to `samtools + zlib` and `samtools + libdeflate` (I had also heard...

mebbert

sambamba-markdup: Unexpected '-' when converting from type string to type ulong

1

I'm getting this error using sambamba/0.5.6 on centOS 7. "sambamba-markdup: Unexpected '-' when converting from type string to type ulong" my command is: sambamba markdup -t --tmpdir $tmpdir $filtered.sorted.bam undup.bam...

ls233