hi everyone
I have an outputted file from vcftools for fst calculation in the following format
CHROM BIN_START BIN_END N_VARIANTS WEIGHTED_FST MEAN_FST
ch1 1 40000 75 0.0516003 0.0355082
ch1 20001 60000 22 -0.00980986 -0.0205035
ch1 40001 80000 46 0.0180676 0.0236424
ch1 60001 100000 72 0.0273771 0.0317944
how can I annotate this file using GTF or GFF file? My goal is to identify possible overlapping genes with detected windows.
Thanks in advance for your help
convert GTF to bed
awk -F '\t' '($3=="gene") {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$9);}' in.gtf
sort both files on chrom and position and then use bedtools intersect
Thank you very much;
based on your recombination I followed:
awk -F '\t' '($3=="gene") {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$9);}' in.gtf > GTF.bed
then
awk '{$4=$5=$6=""; print $0}' vcftools_output.fst > Fst_Windows.bed
bedtools intersect -a GTF.bed -b Fst_Windows.bed > annotated_windows
Is my method correct?
sort both files on chrom and position
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