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

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!

1000genomes vcf
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updated by Ram Ram • written by jxiang15 • jxiang15

Look for TYPE tag.

##INFO=<ID=TYPE,Number=A,Type=String,Description="Type of variant">
• 0 views • link
updated by Ram Ram • written by Ashutosh Pandey Ashutosh Pandey

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

• 0 views • link
updated by Ram Ram • written by jxiang15 • jxiang15

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
• 0 views • link
updated by Ram Ram • written by Jorge Amigo Jorge Amigo

1 answer

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
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updated by Ram Ram • written by Jorge Amigo Jorge Amigo

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.

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updated by Ram Ram • written by jxiang15 • jxiang15

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