SNP data filtering from VCF file

Question

[sukesh1411]

Hi

I am sorry although there are so many questions on this query i could not find the relavant answer. I used vcftools to extract only snps from vcf file using below command

command: vcftools --vcf variantsfilterQDPMQ.vcf --remove-indels --recode --recode-INFO-all --out onlysnps

I got the vcf file which has the information about each nucleotide with snp as well as without snp. I want vcf file only with snp information alone.

I wrote a perl program, its taking lot of time since i got a big vcf file which is 10gb..

Thank you all

[Pierre Lindenbaum]

You have already asked some questions here:

• Realigner Target Creator
• Blast standalone output formatting

please update/comment or validate (green mark on the left) the answers.

[Paul]

Hi, what variant caller do you use? Some of them have an option to call INDELS and SNP separately - for example VarScan..

[sukesh1411]

Hi,

I took vcf file from rice 3000 genome project database. Can i use varscan for exporting only snps from vcf file?

Thanks

[Paul]

Hi, no Varscan is variant caller - it generates VCF from BAM file (mpileup). Did you tried this Pierre solution?

[sukesh1411]

Hi

Thank you Paul... I finished my job using awk script.. thanks to Pierre :)