Converting PED/MAP files to BAM files

Question

[AbdulazizAliQ8]

Hello

I have PED and MAP files that I want to convert to a BAM file. Is that possible?

[Philipp Bayer]

Are you sure you need BAM files? Not BED/FAM/BIM files?

BAM files are normally for storing read alignments, while PED files store just the SNPs in these read alignments. It's practically impossible to get the reads back from your PED files.

[AbdulazizAliQ8]

Hello Philipp,

The reason that I want BAM file is that I am intending to order the yfull.com service for this sample (In case that conversion is possible). I have communicated with yfull.com and they told me they will need BAM files for their analysis.

I read that I can do the (PED/MAP to BED/BIM/FAM) conversion using Plink. For example ( plink --file myPlinkTextData --make-bed --out myPlinkBinaryData )

I wondering if it is possible to then convert BED to BAM for my case.. I came across a software called "bedtools". the following links talks about it:

1- http://bedtools.readthedocs.org/en/latest/content/tools/bedtobam.html

2- https://wiki.hpcc.msu.edu/display/Bioinfo/Converting+BED+to+BAM+Format

[Philipp Bayer]

Hi Abdul,

I don't think this will work out - it looks like yfull wants the raw read alignments (either the raw reads in FASTQ, or the read alignments in BAM).

If you have a PED/MAP file, then you don't have the reads anymore, all you have is the SNPs that were on these reads. You can convert PED via BED to BAM, but you won't get read alignments - converting BED to BAM is just in case you want to store some genomic features in the compressed BAM format for more efficient storage, it won't give you your reads back.

Think of it this way: A genomic read is ~100 base pairs long (BAM, FASTQ), and usually you have only 0-1 SNPs on that read (stored in PED). How do you get the other 99 base-pairs back?

[Pierre Lindenbaum]

Hello AbdulazizAliQ8!

It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=67673

This is typically not recommended as it runs the risk of annoying people in both communities.

[AbdulazizAliQ8]

Hello Pierre, Thanks for letting me know that this is not recommended.

Answer 1

[Govardhan Anande]

I think it is possible with PLINK. Also you can refer similar post here.

Answer 2

[AbdulazizAliQ8]

Thanks Govardhan Anande

Any expert in PLINK who knows how to perform this file conversion? (from PED/MAP to BAM) I need the steps.

Thank you

Answer 3

[AbdulazizAliQ8]

I want to create a BAM file for sample HGDP00146 (from Human Genome Diversity Project)

It is mentioned here:

ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/sample_all_snp.txt

The MAP file: ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/all_snp.map.gz

The PED: ftp://ftp.cephb.fr/hgdp_supp10/Harvard_HGDP-CEPH/all_snp.ped.gz

Can anybody kindly help me with the steps?