keep the variants ID after filteration

Question

[rastogi.suraj93]

Hello everyone, I would like to appreciate if some one help me. I tried to make SNPs ID in VCF file REplace to 0 but facing some problem which occur by commands. my commands is
/SnpEff cat variants.vcf | java -jar SnpSift.jar filter --set my_rs.txt "ID in SET[0]" > filtered.vcf and after getting error like - Exception in thread "main" java.lang.RuntimeException: File not found 'my_rs.txt' so please some one help me where I have to make the mistake for accessing this command ? Thanking you all

Answer 1

[dschika]

Look at the error message:

Exception in thread "main" java.lang.RuntimeException: File not found 'my_rs.txt

The file my_rs.txt is missing

[rastogi.suraj93]

yeah..so please suggest me any other tools and command

[dschika]

From the SnpSift manual:

I want to keep samples where the ID matches a set defined in a file: cat variants.vcf | java -jar SnpSift.jar filter --set my_rs.txt "ID in SET[0]" > filtered.vcf and the file my_rs.txt has one string per line, e.g.:

rs58108140

rs71262674

rs71262673

I don't use SnpSift, but it seems not too complicated: Generate a file called my_rs.txt with one SNP id per line. Do you have that file?

[rastogi.suraj93]

No I dont have. I have vcf file without SNP ID like -

CHROM POS ID REF ALT QUAL

NC_00839 536376 0 TAGCTAGCT TAGCTAGCTAAGCTAGCT 96.5

[dschika]

Well, you wrote

I tried to make SNPs ID in VCF file REplace to 0

Do you have SNP IDs for your SNPs? Do you have a file with 'chromosome position SNP-id'? If you don't have something like this: With what do you want to replace the SNP id??

[rastogi.suraj93]

yeah, in my snp file have chr position but SNP ID is not mention. at the column of ID is mention only 0. I want also give SNP ID in my file like
rs58108140

rs71262674

rs71262673 so how can I give to SNP ID in my vcf file?

[dschika]

Afaik there is 'no automatic SNP id naming tool'.

You could make a SNP-id e.g., consisting of chromosome name and position:

awk '{if ( $1 ~ /^#/ ) {print $0} else {$3 = $1"_"$2; print $0}}' YOUR.vcf > NEW.vcf

[rastogi.suraj93]

Ok, thank you so much. I will try like this.