Script for XP-EHH, EHH and iHS tests and phasing vcf file that works on all chromosome concurrently

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3.7 years ago

taniamahmood38 ▴ 60

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

WGS Pooled-Seq XPEHH EHH iHS • 1.2k views

ADD COMMENT • link 3.7 years ago by taniamahmood38 ▴ 60

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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.

ADD REPLY • link 3.7 years ago by 4galaxy77 2.9k

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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.

ADD REPLY • link 3.7 years ago by taniamahmood38 ▴ 60

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