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Can anyone tell me how to compare the vcf files to find the differences of two or more? Use Existing tools or souce code?
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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
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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
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You can drop the -c argument.Comment
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thank you
let me tryComment
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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
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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
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