Can anyone tell me how to compare the vcf files to find the differences of two or more? Use Existing tools or souce code?
-
-
Originally posted by lyz1030 View Post -
Common snps
which vcftool i can use to find snps that are common between two vcf files.
If there is any other software please recommend
RegardsComment
-
-
vcf-isec
i used vcf-isec to filter snps found in one file but not in other using
./vcf-isec -c -f /home/fisa/orignal_vcf/A.vcf.gz /home/fisa/database_vcf/1kgenome.vcf.gz >/home/huma/lifescope_vcf/A_filtered_1Kgenome.vcf
what changes i need in command to get commonComment
-
You can drop the -c argument.Comment
-
thank you
let me tryComment
-
There's also VAAST if you want to look at more complicated interactions (e.g. SNPs in group 1, but not group 2, unless they're in group 3).Comment
-
vcf-isec error
i used vcf-isec to find common snps between my two files using command
./vcf-isec -f /home/asi/orignal_vcf/A.vcf.gz /home/asi/database_vcf/1Kgenome.vcf.gz >/home/asi/lifescope_vcf/A_common_1Kgenome.vcf
i got this error
Use of uninitialized value $fltr in string ne at ./vcf-isec line 337, <$__ANONIO__> line 74872.
Use of uninitialized value $fltr in string ne at ./vcf-isec line 337, <$__ANONIO__> line 74872.
Any help would be highly appreciatedComment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment