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3.1 years ago
taniamahmood38
▴
50
Hellow, hope all are doing well. I want to ask if there are any scripts for XPEHH, EHH or iHS analysis and to phase the vcf file that can work on all chromosomes simultaneously, I was looking for hapbin for these statistcial tests but that i think works on a single chromosome at a time. Please let me know if there is any script to perform above mentioned tests or to phase the data.
Waiting for the quick reply Thanks in advance
Why do you want to do all chromosomes at once? Since chromosomes are discrete units, it doesn't make sense to analyse them 'as one'. If you have access to a computer with several cores + enough memory you could run them in parallel using e.g. gnu parallel.
Previously, i did FST, HP and Tajima'sD analysis using popoolation2 tool which analyzes all chromosomes at once. Actually, doing it separately would be a cumbersome process. That's why i was trying to find a script or any tool that could perform the analysis on all chromosomes concurrently.