Question: Extract SNPs within 5 bps distance apart
0
gravatar for waqasnayab
2.4 years ago by
waqasnayab180
Pakistan
waqasnayab180 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 • 1.1k views
ADD COMMENTlink modified 2.4 years ago by sacha1.8k • written 2.4 years ago by waqasnayab180
3
gravatar for Pierre Lindenbaum
2.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k 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 2.4 years ago • written 2.4 years ago by Pierre Lindenbaum122k
1

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

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

Cheers,

Waqas.

ADD REPLYlink written 2.4 years ago by waqasnayab180
1
gravatar for Macspider
2.4 years ago by
Macspider2.9k
Vienna - BOKU
Macspider2.9k 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 2.4 years ago • written 2.4 years ago by Macspider2.9k

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 2.4 years ago by waqasnayab180

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

ADD REPLYlink written 2.4 years ago by Pierre Lindenbaum122k
0
gravatar for sacha
2.4 years ago by
sacha1.8k
France
sacha1.8k 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 2.4 years ago by sacha1.8k
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