Finding only biallelic SNPs from the 1000GP BCF files
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4.6 years ago

I want to run some tests on the 1000 Genomes project Phase 3 VCF files:

I downloaded the files from here: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

From these files I only want to keep biallelic SNPs so I want to use the --max-alleles options on vcftools. I've been reading the supporting information to find only SNPs, but I couldn't find a list of them anywhere.

Here's how the file looks:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  NA18525 NA18526 
22  16050075    .   A   G   100 PASS    .   GT  0|0 0|0

EXTRA: Also on the description of the file there is supposed to be information on the ancestral state for each SNP, but I couldn't find that information on the vcf files either.

Here's that line:

##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele. Format: AA|REF|ALT|IndelType. AA: Ancestral allele, REF:Reference Allele, ALT:Alternate Allele, IndelType:Type of Indel (REF, ALT and IndelType are only defined for indels)">
vcf SNP • 1.4k views
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