extract vcf files of each individuals from ALL.chr3.phase1_release_v3.20101123.snps_indels

extract vcf files of each individuals from ALL.chr3.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz using command

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3.6 years ago

Dhara Awasthi ▴ 40

Hey, I want to annotate vcf files from 1000G For further processing using ANNOVAR, i want to extract vcf files of each individual from ALL.chr3.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz using command (someone told me to use vcftools) .....Which command should I use ? PLEASE HELP!!!

Also, I want to further analyse those files using ANNOVAR. Should I do them seperately or should I give the whole mega vcf file (mentioned above) as input?

P.S : My basic question is whether this extraction process necessary for the overall process of annotation?

THANKS in advance!!!

vcf annovar annotation 1000g • 946 views

ADD COMMENT • link 3.6 years ago by Dhara Awasthi ▴ 40

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Should I do them seperately or should I give the whole mega vcf file (mentioned above) as input?

it depends of your downstream analysis....

ADD REPLY • link 3.6 years ago by Pierre Lindenbaum 161k

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see Splitting vcf files to individual samples ; How To Split Multiple Samples In Vcf File Generated By Gatk? ; Split a VCF file into individual sample files ; etc...