vcftools typical usage

[dawe]

Hi all,
I've noticed that vcftools exist... seriously, if you search "vcftools" in seqanswer forum you'll find only 3 threads. BTW I don't want to start a flame about this :-)
I just wonder if anybody here has some experience of these tools and wants to share some usage tips and typical scenarios. vcftools binary comes with many options, and so do the perl scripts. The vcftools pages apparently have no wiki pages (such the samtools or GATK ones)...

d

[adamdeluca]

All I've used it for

vcftools --vcf some1000genomesFile.genotypes.vcf --counts --minDP 3

will give you something like:

CHROM	POS	N_ALLELES	N_CHR	{ALLELE:COUNT}
1	533	2	92	G:87	C:5
1	41342	2	54	T:38	A:16
1	41791	2	62	G:58	A:4
1	44449	2	50	T:48	C:2
1	44539	2	36	C:35	T:1

awk '{print "chr"$1"\t"$2-1"\t"$2"\t"$5"\t"$6}'

and you have a bed file of 1000 genomes variants:

chr1	532	533	G:87	C:5
chr1	41341	41342	T:38	A:16
chr1	41790	41791	G:58	A:4
chr1	44448	44449	T:48	C:2