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Identify SNPs with Fst estimates > 0.9 and annotate them

I have SNPS in the .fst file containing the estimated fst value in the 6th column like:

2R  4459    1   1.000   96.0    1:2=0.01762811
2R  9728    1   1.000   99.0    1:2=0.01340363
2R  9828    1   1.000   100.0   1:2=0.01554609
2R  9928    1   1.000   99.0    1:2=0.01454173
2R  10028   1   1.000   100.0   1:2=0.01317223
2R  10128   1   1.000   100.0   1:2=0.01554917
2R  10228   1   1.000   100.0   1:2=0.01202964
2R  10328   1   1.000   100.0   1:2=0.01316962
2R  10428   1   1.000   100.0   1:2=0.01317223
2R  10528   1   1.000   100.0   1:2=0.01316962
2R  10628   1   1.000   100.0   1:2=0.01778599
2R  10728   1   1.000   100.0   1:2=0.01554609
2R  10828   1   1.000   100.0   1:2=0.01554917

I want to filer those SNPs that have a value greater than 0.9 so I am trying this command in Linux:

awk -F"\t" '$6>0.02' file.fst

But it's not fetching an exact 0.9 from the 6th column due to the presence of 1:2=0 in every row of the 5th column.

Which changes do I need to make in the awk command?

After finding SNPs, I need to annotate them by using snp eff so is it possible to apply SnpEff to the .fst file?

snpeff fst snp
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by anasjamshed anasjamshed

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written by Pierre Lindenbaum Pierre Lindenbaum

2 answers

I don't have much experience using Linux but I use R to do the same thing for which i use this command

library(dplyr)
library(purrr)

FST_file <- read.delim("YourFSTfile.fst")

significatn_snp <- FST_file %>% filter(FST > 0.9)

write.csv(signfificant_snp, "significant_snps.csv", row.names = FALSE)
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written by Yugan Gogul Muthukumar • Yugan Gogul Muthukumar

using '=' as the separator, the column for FST is now the 2nd:

LC_ALL=C awk -F"=" '$2>0.9' file.fst
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written by Pierre Lindenbaum Pierre Lindenbaum

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