SNP data filtering from VCF file
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4.5 years ago
sukesh1411 ▴ 30

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

SNP • 2.2k views
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You have already asked some questions here:

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

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

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Hi,

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

Thanks

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

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Hi

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

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