How to get population specific SNPs from a vcf file
I've got a vcf file and There are 500 individuals in it.Of these 500 individuals, 30 individuals form group A.How can i get all SNPs specific to GroupA (Present in at least one of the 30 individuals and not in the remaining 470).
Looking forward to your answer.
Think you
• 836 views
•
link
updated
by
Pierre Lindenbaum
•
written
by
291796256 •
•
written
by
291796256 •
1 answer
bcftools view --samples-file list-in-groupA.txt -O u in.vcf | bcftools view -i 'AC>0'
• 0 views
•
link
written
by
Pierre Lindenbaum
Log in to answer this question.
More posts like this
-
Splitting VCF by sample: different files but same SNPs number
written by greed •
-
How to Combine Genotype and Phenotype Data?
written by ErickW •
-
Selection of SNPs after imputation
written by Omics data mining
-
Warning: Expected at least 2 parts in INFO entry...while using vcftools, what could be the reason
written by nidhisukhija5 •
-
Pipeline for SNP analysis
written by rebecca08238 •
-
Getting same SNPs both in cancer and normal files when seen in IGV
written by db351223 •
-
Should variant phasing be performed before or after filtering by Minor Allele Frequency?
written by i.wilson •
-
Using VCFtools to find which population codes individuals in a vcf file belong to
written by severalorks
-
What are good settings to filter VCF files to merge SNP data with SNP array data
written by devenvyas
-
ERROR: Stopping as there are no SNPs left for analysis
written by r.asadpur •
