BAM Analysis Kit (Windows and Linux). New release.

[teepean47]

I have released a new version of BAM Analysis kit. Please report any bugs you find!

Highlights:

-Update SNP filters to include more SNPs (23andMe V3 to V5, FTDNA old and new, Ancestry)

-Replace samtools and bcftools with native versions. Htslib has fixed a bug that prevented using native samtools/bcftools. Using native version of samtools speeds up handling large BAM files.

-Remove old mtDNA haplogroup prediction

-Add Yleaf v2 and use it to predict Y-haplogroup

-Update haplogrep to 2.1.20

Download the zip file or use a Git client.

https://github.com/teepean/BAM-Analysis-Kit/releases

I have also released an experimental Linux version of BAM Analysis Kit. Required software: bedtools, samtools 1.7 or higher, bcftools 1.7 or higher, gawk, Python 3.6 or higher with pandas installed

https://github.com/teepean/BAM-Analy...ases/tag/v2.09

[ArmandoR1b]

Windows BAK v2.091 fails for me. I tested it with a random file. Here is the first error with v2.091.

Input BAM : "C:\BAM\Crusades\SI-41.bam"

Pre-execution Cleanup ...

Sorting ...
sort: invalid option -- '@'
open: No such file or directory
[bam_sort_core] fail to open file 4

BAM Analysis Kit 1.8 works fine for the same file. The BAM is in a different directory than the programs.

[Tonev]

Windows BAK v2.091 fails for me. I tested it with a random file. Here is the first error with v2.091.

Input BAM : "C:\BAM\Crusades\SI-41.bam"

Pre-execution Cleanup ...

Sorting ...
sort: invalid option -- '@'
open: No such file or directory
[bam_sort_core] fail to open file 4

BAM Analysis Kit 1.8 works fine for the same file. The BAM is in a different directory than the programs.

Same errors and behaviour for me too...

[teepean47]

I have released a fix, version 2.0.92. For some reason Git did not update the old executables.

https://github.com/teepean/BAM-Analysis-Kit/releases

[xenus]

Were the issues Generalissimo brought up ever addressed?

[teepean47]

Were the issues Generalissimo brought up ever addressed?

If you mean base alignment quality then yes. BAQ is not enabled in samtools or GATK.

I have been working on a new tool based on pileupCaller. The problem with that tool at the moment is that I haven't figured out a decent way to annotate the results.

https://github.com/teepean/FADAK

[xenus]

If you mean base alignment quality then yes. BAQ is not enabled in samtools or GATK.

I have been working on a new tool based on pileupCaller. The problem with that tool at the moment is that I haven't figured out a decent way to annotate the results.

https://github.com/teepean/FADAK

What annotations do you need?
Are you just trying to work pileupCaller into a pipeline?

[teepean47]

What annotations do you need?
Are you just trying to work pileupCaller into a pipeline?

The aim is to replace GATK with pileUpcaller or any other program (snpAD, ANGSD, FreeBayes) suitable for ancient DNA. One aim is to produce Gedmatch compatible files and therefore annotating missing rsids is a necessity. The pipeline has to work on Windows but so far pileupCaller is the only one that is working and is stable for everyday usage. The problem with pileupCaller is that is not multi-threading so could be a lot faster but I have no experience with Haskell.

[xenus]

The aim is to replace GATK with pileUpcaller or any other program (snpAD, ANGSD, FreeBayes) suitable for ancient DNA. One aim is to produce Gedmatch compatible files and therefore annotating missing rsids is a necessity. The pipeline has to work on Windows but so far pileupCaller is the only one that is working and is stable for everyday usage. The problem with pileupCaller is that is not multi-threading so could be a lot faster but I have no experience with Haskell.

If the problem is just parallelizing without shared resources it should be easy. My Haskell ability is rudimentary at best and Haskell's Cabal package manager has always wanted to lock me in dependency hell which I wouldn't imagine to be any nicer on windows.

Seeing that your repo includes Cygwin i'm wondering if that's just because it works better for your use case than WSL or does WSL just not work at all?

[teepean47]

If the problem is just parallelizing without shared resources it should be easy. My Haskell ability is rudimentary at best and Haskell's Cabal package manager has always wanted to lock me in dependency hell which I wouldn't imagine to be any nicer on windows.

Cabal works on Windows. Most of the time. I am currently experimenting with parallel options (RTS+) as pileupCaller is compiled with the -threaded option.

Seeing that your repo includes Cygwin i'm wondering if that's just because it works better for your use case than WSL or does WSL just not work at all?

I am using Windows/Cygwin combination so that the program is more accessible to average users. Linux test version is working fine using WSL.