Question: extract vcf files of each individuals from ALL.chr3.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz using command
0
gravatar for Dhara Awasthi
3 months ago by
Indian Institute of Technology, Jodhpur
Dhara Awasthi20 wrote:

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!!!

annotation 1000g annovar vcf • 158 views
ADD COMMENTlink written 3 months ago by Dhara Awasthi20

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 REPLYlink written 3 months ago by Pierre Lindenbaum133k

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...

ADD REPLYlink written 3 months ago by Pierre Lindenbaum133k

Thank you for your response!!!

ADD REPLYlink written 3 months ago by Dhara Awasthi20
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