How do we distinguish between SNP/INDEL/SV in 1000 genomes Phase 3 data

Question

[jxiang15]

Hello,

I'm trying to switch to using the Phase 3 1000 genomes data from Phase I. In phase I, there was a indicator that said the variant type, so you could for example filter out SNPs easily with a grep command. However, they remove the below from Phase 3.

• VT=SNP, indicates the variant is a snp.
• VT=INDEL, indicates the variant is an indel,
• VT=SV, indicates the variant is a deletion.

Anyone know if there's an easy way to filter out the SNPs? Is there another indicator in the file that I'm missing?

Thanks!

[Pierre Lindenbaum]

help us, where is the VCF please?

[jxiang15]

Here's phase I

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20110521

and here's phase 3

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/

Thanks

[Ashutosh Pandey]

Look for TYPE tag.

##INFO=<ID=TYPE,Number=A,Type=String,Description="Type of variant">

[jxiang15]

I don't think there's a tag like that in these files.

[Jorge Amigo]

Strangely, there isn't such "TYPE" tag on latest 1000genomes phase3 data (well, it is on the X chromosome).

If you are still willing to build a grep-like query:

for file in ALL.chr*.vcf.gz; do zcat $file | grep -P "\t[ACGT]\t[ACGT]\t" > ${file/.vcf.gz/.snps.vcf.gz}; done<

I would go for perl though:

for file in ALL.chr*.vcf.gz; do zcat $file | perl -lane 'print if /\t[ACGT]\t[ACGT]\t/' > ${file/.vcf.gz/.snps.vcf.gz}; done

Answer 1

[Jorge Amigo]

bcftools allows you to filter variants by type using option -v, --types snps|indels|mnps|other (comma-separated list of variant types to select), plus it generates perfectly well-formed vcf output files. for this last reason, and for its great performance (latest HTSlib 1.1 core works like a charm), I would definitely recommend it instead of grep for parsing vcf files. as easy as this simple command:

bcftools view -v snps all.variants.vcf > snps.only.vcf

[jxiang15]

Thanks, I'm try that. However, bcftools is probably looking for a tag just like I am. It would be great to know what it's looking for when doing the filtering. Also, is there a particular reason you like bcftools instead of vcftools, just curious.

[Jorge Amigo]

bcftools is faster. it is even stated in the vcftools Perl tools and API page, and roughly described on a small section of the vcftools site.