Hi there all! I have 2 vcf files with filtered SNPs and now I want to extract a. The genes that are shared between the 2 vcf files b. The SNPs that are different on the shared genes between these two vcf files. for example 1.vcf
TRINITY_DN17985_c2_g1 539 0 G A
TRINITY_DN17985_c2_g1 576 0 G A
TRINITY_DN17985_c2_g1 710 0 A T
TRINITY_DN17985_c2_g1 722 0 T C
TRINITY_DN17985_c2_g1 822 0 A G
TRINITY_DN17985_c2_g1 1608 0 T G
TRINITY_DN17985_c2_g1 2353 0 T A
TRINITY_DN17985_c2_g1 4371 0 T A
TRINITY_DN17985_c2_g1 6200 0 C T
TRINITY_DN17985_c2_g1 7444 0 G T
TRINITY_DN17985_c2_g1 7456 0 A T
TRINITY_DN17985_c2_g1 2434 0 G T
TRINITY_DN17985_c2_g1 4190 0 G A
TRINITY_DN17985_c2_g1 4275 0 A G
TRINITY_DN15509_c1_g1 626 0 A C
TRINITY_DN15509_c1_g1 1647 0 G A
TRINITY_DN15425_c1_g4 741 0 G A
TRINITY_DN12988_c0_g1 1553 0 T A
TRINITY_DN14521_c2_g1 826 0 T A
2.vcf
TRINITY_DN17985_c2_g1 539 0 G T
TRINITY_DN17985_c2_g1 576 0 G T
TRINITY_DN17985_c2_g1 710 0 A G
TRINITY_DN17985_c2_g1 722 0 T C
TRINITY_DN17985_c2_g1 822 0 A G
TRINITY_DN17985_c2_g1 1608 0 T G
TRINITY_DN17985_c2_g1 2353 0 T A
TRINITY_DN17985_c2_g1 4371 0 T A
TRINITY_DN17985_c2_g1 6200 0 C T
TRINITY_DN17985_c2_g1 7444 0 G T
TRINITY_DN17985_c2_g1 7456 0 A T
TRINITY_DN16743_c0_g1 5739 0 G A
TRINITY_DN16743_c0_g1 5764 0 T A
TRINITY_DN16743_c0_g2 199 0 A T
TRINITY_DN16295_c0_g1 982 0 A G
and I want to extract only the following for which the ALT allele is different between 1.vcf and 2.vcf files.
TRINITY_DN17985_c2_g1 539 0 G A
TRINITY_DN17985_c2_g1 576 0 G A
TRINITY_DN17985_c2_g1 710 0 A T
TRINITY_DN17985_c2_g1 539 0 G T
TRINITY_DN17985_c2_g1 576 0 G T
TRINITY_DN17985_c2_g1 710 0 A G
I know that I can use bcftools isec for getting the SNPs that are shared between the two or the SNPs that are unique in the first and second file respectively. But how I can get first the genes that are present in both files?
Thanks a lot in advance for any help! Sofia
•
written
by
paraskevopou •
1 answer
If the first column is the "genes", then:
bedtools intersect -wa -wb -a 1.vcf -b 2.vcf > shared.vcf
grep -v '^#' shared.vcf | cut -f1 -d' ' shared.vcf | sort | uniq # list of unique genes
Then, assuming it's the same reference (ie ref is the same on the same position) and that both vcf files actually have 10 columns:
grep -v '^#' shared.vcf | awk '$5!=$15' > diff.vcf # differing positions, no header
Of course, depending on what you want to do with that file afterwards, you may want to restore the header and remove columns 11-20 (or add them as new rows etc).
Log in to answer this question.
-
Infer ancestry for RNA-seq data
written by Matthew Chang •
-
bcftools merge without multiallelic sites
written by octpus616 •
-
PLINK .ped file from vcf file with 2 alleles
written by Liubov •
-
calculate fst for every allele in any position
written by mostafarafiepour
-
How to merge vcf files
written by xiaohuanlu111 •
-
Extract columns from a vcf file using identifiers from a second file
written by paraskevopou •
-
SNP annotation from RNA-seq data without referene
written by paraskevopou •
-
supertranscripts (conceptual question)
written by paraskevopou •
-
Comparing vcf files
written by paraskevopou •
-
Plotting common SNPs from four individual from a vcf file
written by vicky •
I suppose this is not the format that the post should have. The VCF format doesn't look like a VCF format. Can you please wrap it around the code flag? (little button with 101010)
I have just done that (wrapped it in code format)