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+---- Thread: Release: BAM to plink (/showthread.php?tid=645)
Release: BAM to plink - teepean - 03-16-2024
So I have had questions over the years about creating datasets and here I present a new program called aDNA to dataset (AKA make-myself-redundant)
There are both Linux and Windows versions available. The instructions are very simple so I would like to get feedback from anyone interested in creating their own datasets from BAMs.
Notice: Windows version includes all the files necessary to run except references. For Linux you need to have samtools and pileupCaller in your path.
pileupCaller can be downloaded from here and for samtools I assume you know how to use apt, pacman, yum etc.
https://github.com/stschiff/sequenceTools
Main page:
https://github.com/teepean/adna_to_dataset
Download:
https://github.com/teepean/adna_to_dataset/archive/refs/tags/v.0.2.zip
PileupCaller uses default settings and if you want to modify them you have to edit the .bat or .sh.
EDIT: the program supports only hs37d5 and hg19 as references as those are the most commonly used in aDNA papers. hg38/T2T support can be added if AADR starts supporting those references.
RE: Release: BAM to plink - Qrts - 03-16-2024
Brilliant work. Thank you for your contributions teepean.
RE: Release: BAM to plink - teepean - 03-16-2024
New release that includes a reference downloader.
https://github.com/teepean/adna_to_dataset/archive/refs/tags/v.0.3.zip
RE: Release: BAM to plink - ChrisR - 03-17-2024
(03-16-2024, 05:37 PM)teepean Wrote: So I have had questions over the years about creating datasets and here I present a new program called aDNA to dataset (AKA make-myself-redundant)
There are both Linux and Windows versions available. The instructions are very simple so I would like to get feedback from anyone interested in creating their own datasets from BAMs.
Notice: Windows version includes all the files necessary to run except references. For Linux you need to have samtools and pileupCaller in your path.
EDIT: the program supports only hs37d5 and hg19 as references as those are the most commonly used in aDNA papers. hg38/T2T support can be added if AADR starts supporting those references.
Sorry for n00b question but what is the main purpose of creating own datasets from BAMs?
Regarding references download etc. may I ask if this could be installed together with WGSExtract so that big (reference) files/paths can be shared?
RE: Release: BAM to plink - miquirumba - 03-17-2024
(03-16-2024, 05:37 PM)teepean Wrote: So I have had questions over the years about creating datasets and here I present a new program called aDNA to dataset (AKA make-myself-redundant)
There are both Linux and Windows versions available. The instructions are very simple so I would like to get feedback from anyone interested in creating their own datasets from BAMs.
Notice: Windows version includes all the files necessary to run except references. For Linux you need to have samtools and pileupCaller in your path.
pileupCaller can be downloaded from here and for samtools I assume you know how to use apt, pacman, yum etc.
https://github.com/stschiff/sequenceTools
Main page:
https://github.com/teepean/adna_to_dataset
Download:
https://github.com/teepean/adna_to_dataset/archive/refs/tags/v.0.2.zip
PileupCaller uses default settings and if you want to modify them you have to edit the .bat or .sh.
EDIT: the program supports only hs37d5 and hg19 as references as those are the most commonly used in aDNA papers. hg38/T2T support can be added if AADR starts supporting those references.
Do you think it could be possible a T2T CHM13 liftover of AADR data? Plink 2 can work perfectly with CHM13 reference and many low coverage ancient DNA raw data detects more SNPs with CHM13 reference alignment
RE: Release: BAM to plink - teepean - 03-17-2024
(03-17-2024, 12:57 PM)ChrisR Wrote: Sorry for n00b question but what is the main purpose of creating own datasets from BAMs?
Regarding references download etc. may I ask if this could be installed together with WGSExtract so that big (reference) files/paths can be shared?
The idea is that more people could create datasets. As for the references it is possible to edit the code to point to a different location.
..\winbin\samtools mpileup -B -q 30 -Q 30 -l ../positions/v42.4.1240K.pos -f ../reference/hs37d5.fa
RE: Release: BAM to plink - Kale - 03-17-2024
Excellent! This sounds very useful. Quick question, about how much RAM does this program utilize on Windows, and is it compatible with 32-bit OS?
RE: Release: BAM to plink - Fabrice E - 03-17-2024
ok
Technical question from a noob :
I am running the program from Windows. The download for the references starts without any issues. Then, I encounter the question "enter population name". Which population does this refer to?
RE: Release: BAM to plink - Anglesqueville - 03-17-2024
(03-17-2024, 05:05 PM)Fabrice E Wrote: ok
Technical question from a noob :
I am running the program from Windows. The download for the references starts without any issues. Then, I encounter the question "enter population name". Which population does this refer to?
The outcome is a PLINK packedped consisting of 3 files (.bed, .bim, .fam) that will be created in the target subdirectory. The .fam indicates for each individual a Population Name and an Individual Name. These are what the program asks you to choose.
RE: Release: BAM to plink - TanTin - 03-18-2024
Can someone convert these 2 files to plink please?
GRC13292545.chrY.bam
GRC13292546.chrY.bam
https://evolbio.ut.ee/chrY/
These are Y chromosomes of A00 used by Karmin et al. (2015) .
RE: Release: BAM to plink - TanTin - 03-18-2024
In addition , these BAM files are hg18 ( not hg19) .
##reference=file:///cvmfs/data.galaxyproject.org/byhand/hg18/sam_index/hg18.fa
The snp positions POS ID are not the same as hg19.
RE: Release: BAM to plink - teepean - 03-19-2024
(03-18-2024, 01:57 PM)TanTin Wrote: Can someone convert these 2 files to plink please?
GRC13292545.chrY.bam
GRC13292546.chrY.bam
https://evolbio.ut.ee/chrY/
These are Y chromosomes of A00 used by Karmin et al. (2015) .
This program should not be used for Y-DNA.
RE: Release: BAM to plink - teepean - 03-19-2024
New version released with reference auto-detection:
https://github.com/teepean/adna_to_dataset/archive/refs/tags/v.0.5.zip