# 1- calculate individual homozygosity with vcftools
# 1- calculate individual homozygosity with vcftools
# 2- calculate individual heterozygosity in R
# 2- calculate individual heterozygosity in R
# 3- inspect values and keep only individuals with non-extreme values
# 3- inspect values and keep only individuals with non-extreme values
# extreme values are defined as those that fall outside of 9 times the interquartal range. (typical outliers are defined as 1.5IQR) this was set arbitrarily after visual inspection, and to allows the same criteria to be applied to both species
# extreme values are defined as those that fall outside of 6 times the interquartal range. (typical outliers are defined as 1.5IQR)
# this was set arbitrarily after visual inspection, and to allow the same criteria to be applied to both species
@@ -39,44 +39,6 @@ bash filtering.sh ../00-rawData/02-Mullus/mullus.vcf 02-Mullus mul
...
@@ -39,44 +39,6 @@ bash filtering.sh ../00-rawData/02-Mullus/mullus.vcf 02-Mullus mul
The final step consists of removing individuals with (extreme) outlier heterozygosity values. Here we define outliers as falling outside 6 * interquartile range.
The final step consists of removing individuals with (extreme) outlier heterozygosity values. Here we define outliers as falling outside 6 * interquartile range.
This theshold value is set in accordance to our data and it is advised to look at the outputted figures to validate this choice for your data.
This theshold value is set in accordance to our data and it is advised to look at the outputted figures to validate this choice for your data.
### SNP filtering results for Mullus surmuletus
| filtering step | filter for | individuals retained | SNPs retained | run time (sec) | output |