hi everyone
i am trying to annotate of identified SNPs and INDELs (vcf format) using software such as snpEff. i downloaded gff3 file correspond to my reference genome. i have to build database in snpEff because my desired database is not present in snpEff.
problem: scaffold names in gff3 file and VCF file are different and i must to convert scaffold names in gff3 file to scaffolds name in VCF file and then try to building new database in snpEff using name-converted gff3 file. anybody here know how i can do it?
example of differences in scoffold names
name in gff3 * name in VCF
NW_011590949.1 * KN271049.1
NW_011590950.1 * KN271050.1
...
are there alternative ways to annotate new SNPs? it is possible to merge gff and VCF to annotate VCF file?
thanks in advance
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reza
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Hi
This is an example of what I used. It worked for me.
awk '{gsub(/Ld01_v01s1/, "1"); gsub(/Ld02_v01s1/, "2"); gsub(/Ld03_v01s1/, "3"); gsub(/Ld04_v01s1/, "4"); gsub(/Ld05_v01s1/, "5"); gsub(/Ld06_v01s1/, "6"); gsub(/Ld07_v01s1/, "7"); gsub(/Ld08_v01s1/, "8"); gsub(/Ld09_v01s1/, "9"); gsub(/Ld10_v01s1/, "10"); gsub(/Ld11_v01s1/, "11"); gsub(/Ld12_v01s1/, "12"); gsub(/Ld13_v01s1/, "13"); gsub(/Ld14_v01s1/, "14"); gsub(/Ld15_v01s1/, "15"); gsub(/Ld16_v01s1/, "16"); gsub(/Ld17_v01s1/, "17"); gsub(/Ld18_v01s1/, "18"); gsub(/Ld19_v01s1/, "19"); gsub(/Ld20_v01s1/, "20"); gsub(/Ld21_v01s1/, "21"); gsub(/Ld22_v01s1/, "22"); gsub(/Ld23_v01s1/, "23"); gsub(/Ld24_v01s1/, "24"); gsub(/Ld25_v01s1/, "25"); gsub(/Ld26_v01s1/, "26"); gsub(/Ld27_v01s1/, "27"); gsub(/Ld28_v01s1/, "28"); gsub(/Ld29_v01s1/, "29"); gsub(/Ld30_v01s1/, "30"); gsub(/Ld31_v01s1/, "31"); gsub(/Ld32_v01s1/, "32"); gsub(/Ld33_v01s1/, "33"); gsub(/Ld34_v01s1/, "34"); gsub(/Ld35_v01s1/, "35"); gsub(/Ld36_v01s1/, "36"); print;}' ~/Documents/LeishGenomeInfo/Ldonovani_BPK282A1.noseq.gff3 > ~/Documents/LeishGenomeInfo/Ldonovani_BPK282A1.noseq-new.gff3
Rangi
Instead of using this method, it may be more efficient to 1. sort your files according to the chromosome names and then 2. use the unix join command, which performs an SQL style join on two files and 3. cut the columns from your resulting joined file using the unix cut command to get the final file that you want to have.
Instead of modifying the GFF, it's probably easier to add the new scaffold names to your VCF using VCFtools or BCFtools 'annotate' and then edit the VCF to replace the scaffold names.
EDIT: Even easier, assuming you have a file with OLD_NAME and NEW_NAME fields, is the Linux 'join' command:
join -o 1.2,2.2,2.3,2.4,2.5,2.6,2.7,2.8 OLD_NEW_NAMES.FILE OLD.VCF > NEW.VCF
Note that, for any old scaffold name without a corresponding new name, those variants will be lost. Also, you will need to copy the OLD.VCF header to the new file.
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It's weird that you have different scaffolds names taking in to account that it is the same genome. Are you sure that the genome you have used for variant calling is the same genome that it is annotated in the gff3 file? same genome and same version? If the answer is
yes, if you have list withgff3 - vcf scaffold name correlation, let's sayNW_011590949.1gff3 scaffold correspond toKN271049.1vcf scaffold, it shouldn't be so difficult to change the names using a little script or awk command.