Single VCF file with multiple populations from 1000 genome project

Question

[JstRoRR]

Hi,

We have identified SNPs in biological replicates (x3) for each population (in vcf files) from RNA-Seq data. My question is: how do we calculate the SNP frequency for each population from pooling the individual biological replicates?

I have found a VCF format in 1000 genomes project for describing all the population in one one VCF file with their respective pooled allele frequencies.

1 15211 rs78601809 T G 100 PASS AC=3050;AF=0.609026;AN=5008;NS=2504;DP=32245;EAS_AF=0.504;AMR_AF=0.6772;AFR_AF=0.5371;EUR_AF=0.7316;SAS_AF=0.6401;AA=t|||;VT=SNP

Our format is:

Sample 1  rep1
Sample 1  rep2
Sample 1  rep3
Sample 2  rep1
Sample 2  rep2
Sample 2  rep3

We have individual VCF file for each replicate from each sample. I just don't have any idea how to put all the reps information in single VCF file and get a pooled AF for each sample like in the format above.

Many thanks.

[st.ph.n]

You can use vcf-tools, vcf-merge, to create a single vcf file using all individual vcf files as inputs. How Can I Merge A Large Amount Of Vcf Files?

[JstRoRR]

Hi Stephen, Thanks for your reply. Simple merging wont solve my problem. Will I get per sample (pooled from replicates) Allele frequencies as highlighted in above example?

[st.ph.n]

You'll get new columns with the info for each sample in separate columns, placed at the end of each line for each site.

[JstRoRR]

Thanks Stephen.