Variant frequency calculation
I have generated a multisample vcf file and also I have calculated each variant frequency across the samples using VCF tools as follows.
chr start end Ref Alt inhouseFreq
1 13418 13418 G A 0.231884
1 13494 13494 A G 0.00483092
1 13504 13504 G A 0.00241546
1 13525 13525 G T 0.00724638
1 13537 13537 C T 0.00966184
Along with frequency, I would also like to count homozygous and heterozygous states of each variant across the sample. Please give some suggestions regarding this.
• 3,137 views
•
link
written
by
nkausthu •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
BCFtools isec output vs BCFtools query
written by gtho123
-
Converting custom VCF to standard VCF
written by avelarbio46 •
-
how to add a column summarizing in which samples the variant was identified
written by Adham •
-
VCF filtering based on AB (Allele-Balance) tag
written by AISHA
-
How realible samtools/ bam-readcount /igvtools /pysamstats for finding deletions/insertions?
written by IrK
-
Is there a tool that can output the raw genotype call (i.e., 0/1) rather than the actual basecall (…
written by mmats010 •
-
Genotype dosage from VCF genotype likelihoods
written by lkw222 •
-
Perl script for reformatting a plink/seq output file
written by plink_9857
-
Piloting population frequencies of different populations
written by kv.shamsudheen •
-
Help With Genotyping In My Vcf File
written by Paul
One tool that might work is CRAVAT (http://www.cravat.us ). I believe it should show the zygosity of variants and frequency if you submit a VCF file.
@ nkausthu, could you show which parameter of VCFtools that calculate variant frequency? What you have done is exactly what I wanted to do. Thanks!