Question: filtering vcf file
1
gravatar for kk.mahsa
2.1 years ago by
kk.mahsa100
kk.mahsa100 wrote:

what program can do filter vcf file with below creteria? which program give me mean and SD of read depth?

i) SNPs and indels with overall quality less than 20; (ii) variants with very low or very high read depth. First we calculated the mean and standard deviation read depth for all the variants. We then set the minimum acceptable coverage as 10% of the mean and the maximum acceptable coverage as the mean read depth plus three times the standard deviation; (iii) variants with less than one forward or reverse alternative allele read; (iv) variants within 5 bp of each other; (v) SNPs within 5 bp of an indel; (vi) indels within 10 bp of each other.

snp next-gen vcf • 808 views
ADD COMMENTlink modified 2.1 years ago by Alex Reynolds28k • written 2.1 years ago by kk.mahsa100

what have you tried ?

ADD REPLYlink written 2.1 years ago by Pierre Lindenbaum119k
1

i am trying to filter my vcf file (resulted from WGS) with mentioned creteria. what is your suggestion Pierre?

ADD REPLYlink written 2.1 years ago by kk.mahsa100
1

i can filter vcf file with criteria such as DP, QUAL, MQ, PL using SnpSift. But writing script for mentioned criteria is hard to me.

ADD REPLYlink written 2.1 years ago by kk.mahsa100
1
gravatar for Patrick Brennan
2.1 years ago by
Toledo, OH USA
Patrick Brennan40 wrote:

You could check out VCFtools at http://vcftools.sourceforge.net/. Otherwise, you might have to write your own script.

ADD COMMENTlink written 2.1 years ago by Patrick Brennan40
1
gravatar for Alex Reynolds
2.1 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

Convert to BED with BEDOPS vcf2bed and then do set operations with bedops and bedmap etc. on the output.

$ vcf2bed --insertions in.vcf > insertions.bed
$ vcf2bed --deletions in.vcf > deletions.bed
$ vcf2bed --snvs in.vcf > snvs.bed

http://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html

http://bedops.readthedocs.io/en/latest/content/reference/set-operations/bedops.html

http://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html

http://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Alex Reynolds28k
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