Question: Extract SNPs within 5 bps distance apart
0
gravatar for waqasnayab
9 weeks ago by
waqasnayab110
Pakistan
waqasnayab110 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 • 237 views
ADD COMMENTlink modified 9 weeks ago by sacha740 • written 9 weeks ago by waqasnayab110
3
gravatar for Pierre Lindenbaum
9 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum94k 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 9 weeks ago • written 9 weeks ago by Pierre Lindenbaum94k
1

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

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

Cheers,

Waqas.

ADD REPLYlink written 9 weeks ago by waqasnayab110
1
gravatar for Macspider
9 weeks ago by
Macspider1.1k
Vienna - BOKU
Macspider1.1k 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 9 weeks ago • written 9 weeks ago by Macspider1.1k

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 9 weeks ago by waqasnayab110

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

ADD REPLYlink written 9 weeks ago by Pierre Lindenbaum94k
0
gravatar for sacha
9 weeks ago by
sacha740
France
sacha740 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 9 weeks ago by sacha740
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