help with format of hapotype snp files

Question

[biloubilar]

Hello,

i am a student in phD and i am starting to work with SNP in my project.

i realized that i have source of infromation about my SNP in different format, from 1000 genomes, some generated by myself from my sequencing data and others from collaborators that send us files in HAPS format.

I would like to know if there is a software or an easy way to convert all my differents file and fused them to have finally only one file to work with and to study with some software of haploptype.

I am starting in bioinformatics so if you could provide me some advice i would appreciate. If you need more information i will provide them.

Thank you very much. bilou

Answer 1

[Kevin Blighe]

I would encourage you to transform everything into a PLINK dataset and then merge them within PLINK.

For conversion of HAPS to PLINK format, take a look here:

• How Can I Convert Impute2 (.Haps .Sample) To Plink (.Map .Ped)?
• File format reference - haps (Oxford phased haplotype file)

If you have data in VCF or BCF, and also for merging datasets within PLINK, take a look at my tutorial here: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format

Kevin

Answer 2

[biloubilar]

Thank you very much for your answer,

i will try your advice and tell you if it is fine.

Thank you again. bilou