Question: Extract SNPs within 5 bps distance apart
0
gravatar for waqasnayab
8 months ago by
waqasnayab140
Pakistan
waqasnayab140 wrote:

Hi,

I am wondering is there a way to extract / print those variants from a vcf file whose distance is not more than 5 bps apart?

Regards,

Waqas.

snp next-gen R vcf • 393 views
ADD COMMENTlink modified 8 months ago by sacha820 • written 8 months ago by waqasnayab140
3
gravatar for Pierre Lindenbaum
8 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum100k wrote:

If I'm not wrong, you can flag the close SNPs with: https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php

java -jar /commun/data/packages/gatk/3.7.0/GenomeAnalysisTK.jar -T VariantFiltration -R ref.fasta -V input.vcf --clusterSize 2 --clusterWindowSize  5

this will add 'SnpCluster' in the FILTER column.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Pierre Lindenbaum100k
1

Yes, Pierre GATK's VariantFiltration worked for me. I wanted the exact same thing...,,,!!!!

Big Thanks...,,,,!!!!

Cheers,

Waqas.

ADD REPLYlink written 8 months ago by waqasnayab140
1
gravatar for Macspider
8 months ago by
Macspider1.6k
Vienna - BOKU
Macspider1.6k wrote:

Yes, you can do it in many ways (python, command line, perl). You just have to ask for this condition to be verified:

for each line, print line if (line_position - previous_line_position) <= 5

The position field in the VCF file is the 2nd :) https://samtools.github.io/hts-specs/VCFv4.2.pdf

ADD COMMENTlink modified 8 months ago • written 8 months ago by Macspider1.6k

yeah, chromosomal positions (second column) is my target. I searched on google but I failed. Is there a way, to do the same in awk?

Thanks,

Waqas.

ADD REPLYlink written 8 months ago by waqasnayab140

yes, but it's more complicated with indels/multi-allelic sites + check the chromosome is the same.

ADD REPLYlink written 8 months ago by Pierre Lindenbaum100k
0
gravatar for sacha
8 months ago by
sacha820
France
sacha820 wrote:

I guess you can do it with bedtools cluster in two step. http://bedtools.readthedocs.io/en/latest/content/tools/cluster.html?highlight=cluster

ADD COMMENTlink written 8 months ago by sacha820
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 938 users visited in the last hour