readme.seekparentf90
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readme.seekparentf90 [2018/07/21 01:03] – [Optional arguments] ignacio | readme.seekparentf90 [2020/03/31 16:00] – ignacio | ||
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Program '' | Program '' | ||
- | | + | |
and Wiggans et al 2010 JDS | and Wiggans et al 2010 JDS | ||
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< | < | ||
- | check for duplicate | + | check for duplicate |
Optional parameter //thr// changes the default threshold to identify duplicate samples (default 0.9) | Optional parameter //thr// changes the default threshold to identify duplicate samples (default 0.9) | ||
+ | |||
+ | < | ||
+ | check for duplicate samples only for individuals in the specified //file// across the full genotype file. \\ | ||
+ | Optional parameter //thr// changes the default threshold to identify duplicate samples (default 0.9) | ||
+ | |||
=====Chip and SNP information===== | =====Chip and SNP information===== | ||
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If more than one chip is used then the number of SNP in common for two samples (base on both chips) will be used for check conflict and for discovering of parents. | If more than one chip is used then the number of SNP in common for two samples (base on both chips) will be used for check conflict and for discovering of parents. | ||
- | ====Other options==== | ||
- | < | ||
- | Select the SNP in common between all chips to be used in the analyses | ||
- | |||
- | < | ||
- | Only the list of SNP names in //file// will be included in the analyses | ||
- | |||
- | < | ||
- | The list of SNP names in //file// will be excluded from analyses | ||
- | |||
- | |||
- | < | ||
- | Only SNP in Chromosomes //n1 n2, etc// will be included in the analyses | ||
- | |||
- | < | ||
- | SNP in Chromosomes //n1 n2, etc// will be excluded from analyses | ||
- | |||
- | < | ||
- | Indicate that the //n// chromosome | ||
====Example==== | ====Example==== | ||
Consider a genotype file with 4 samples and 3 chips with the following number of SNP:\\ | Consider a genotype file with 4 samples and 3 chips with the following number of SNP:\\ | ||
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</ | </ | ||
| | ||
+ | |||
+ | ====Other options==== | ||
+ | < | ||
+ | Select the SNP in common between all chips to be used in the analyses | ||
+ | |||
+ | |||
+ | < | ||
+ | Only the list of SNP names in //file// will be included in the analyses | ||
+ | |||
+ | < | ||
+ | The list of SNP names in //file// will be excluded from analyses | ||
+ | |||
+ | |||
+ | < | ||
+ | Only SNP in Chromosomes //n1 n2, etc// will be included in the analyses | ||
+ | |||
+ | < | ||
+ | SNP in Chromosomes //n1 n2, etc// will be excluded from analyses | ||
+ | |||
+ | < | ||
+ | Indicate that the //n// chromosome | ||
=====Output files===== | =====Output files===== |
readme.seekparentf90.txt · Last modified: 2024/03/25 18:22 by 127.0.0.1